In the grand scheme of things time signature doesn't really matter as long as it all works out for you and anyone else playing with you.  In larger orchestral arrangements it's helpful so that everybody can refer to the same places when the conductor says something like "let's pick up at measure 99".  Since everyone is in the same time signature they are all in the correct place for measure 99.
 
The reason I lean toward 4/4 for that first song is because the kick/snare pattern is established before anything else and counting in multiples of four from the beginning of the track makes the synth pad land on the one when it starts.  If you count in multiples of 6 then the pad starts on a 5.  Then again that may have been the composers intention--or maybe that's not the very beginning of the song.  I've been known to start songs in weird spots.  It helps create tension.
 
The pattern in that first song is very similar to bossa nova--not exactly, but similar.
 
The bass player in my band tends to count things in weird ways--he'll hear 3/4 especially in patterns similar to what you presented.  I will sometimes subdivide a beat in my head so that I don't go insane trying to count an eight or sixteenth note pattern.  As long as it sounds good--it is good.

I guess it makes a difference if you're trying to arrange with something like Jamstix though. Although in that case, experimentation is the key.

I too would probably count the intro in 4/4 but then, assuming I am playing it live and I have license to improvise or embellish, I would start counting in 6/4 (i.e., two measures of 6/4 versus three measures of 4/4). 
 
1 & 2 & 3 & 4 &  | 1 & 2 & 3 & 4 & | 1 & 2 & 3 & 4 &
1 & 2 & 3 & 4 &  | 5 & 6 & 1 & 2 & | 3 & 4 & 5 & 6 &
 
The advantage from a drummers perspective is the way the accents and fills would fall against the count going on inside my head.  It might be easier to do a fill on counts 5 and 6 and crash on 1 ... than fill on 1 and 2 and crash on 3.  From a book keeping point of view, it makes no difference but from a playing perspective it may make a difference to the individual player and as vanblah said:
 

In the grand scheme of things time signature doesn't really matter as long as it all works out for you and anyone else playing with you. 

 
My funniest example of making up a count to fit is how I played the intro to Zep's Rock and Roll when I was a young man.  I am not kidding you, I would literally count the number of beats between accents ... until later in life I understood it as nothing more than a Chuck Berry intro without the melody. 
 
1 2 3    1 2 3 4 5 1 2 3    1 2 3 4 5  1 2 3    1 2 3 4  1 2 3 1   2  1  2 3 1 2 3 4
& 4 & | 1 & 2 & 3 & 4 & | 1 & 2 & 3 & 4 & | 1 & 2 & 3 & 4 & | 1 & 2 & 3 & 4 &
 
The top line is the way I used to count it, and the bottom line is what is going on inside my head today (the listener would not be able to tell the difference).
 
[BOLD indicates accent]

sharke
Yeah I guess that's what's making me hear both....the kick is playing in 2/4 and the melodic elements are phrased in 3/4. I have these confusions when trying work out what time sig my own music is in all the time. 

Those who have suggested the composit is 6/4 are probably correct ... that is, if you had to translate this to a printed score.  Thinking just in terms of DAW "rendering", it's more logical to think of a repeating pattern (a groove clip if you like) that has the percussion pattern on one track and something completely unrelated time-sig-wise on the rest of the tracks.  And that "groove clip" is definitely two measures of 2/4.  In the context of 6/4, the percussion pattern is identical in the first, second and third portions of every 6/4 measure.

If there had to be one time signature.  It would have to be two-four.  The six pattern loop comes in after 8 bars of two-four so the entrance would make no sense in this simplistic looping musical context. 
 
More likely though, the "composer" just isn't very good and has no idea what pattern he/she intended.  So take your pick.  I vote for a time sig change 8 bars in to six-four.

rumleymusic
If there had to be one time signature.  It would have to be two-four.  The six pattern loop comes in after 8 bars of two-four

How do you know the time sig isn't 6/4 with the first beat in the first measure measure starting on beat 3? 

rumleymusic
More likely though, the "composer" just isn't very good and has no idea what pattern he/she intended.  So take your pick.  I vote for a time sig change 8 bars in to six-four.

I wouldn't say that the composer isn't very good, it's just that he's probably like me and plays with stuff until it sounds good regardless of any considerations of correctness. He was in one of Future Music's "In The Studio With..." videos on YouTube not so long ago and he gave me that impression anyway. He seems like a bit of a scatterbrain....in the best possible way. 
 
I used to listen to a lot of folk music (English, Scottish, Irish) and it's very often all over the place time sig wise...like the old blues singers, they'll just throw in the occasional extra beat when they feel like, usually to fit the lyrics. I once heard folk guitarist Martin Carthy say that he considers a lot of his music to be in 1/1 time...i.e. just take it as it comes.
 
And then of course there's Frank Zappa. 

dmbaer

rumleymusic
If there had to be one time signature.  It would have to be two-four.  The six pattern loop comes in after 8 bars of two-four

How do you know the time sig isn't 6/4 with the first beat in the first measure measure starting on beat 3? 

Indeed.  Also, an intro doesn't have to follow the same pattern as the rest of the song.

sharke

rumleymusic
More likely though, the "composer" just isn't very good and has no idea what pattern he/she intended.  So take your pick.  I vote for a time sig change 8 bars in to six-four.

I wouldn't say that the composer isn't very good, it's just that he's probably like me and plays with stuff until it sounds good regardless of any considerations of correctness. He was in one of Future Music's "In The Studio With..." videos on YouTube not so long ago and he gave me that impression anyway. He seems like a bit of a scatterbrain....in the best possible way. 
 
I used to listen to a lot of folk music (English, Scottish, Irish) and it's very often all over the place time sig wise...like the old blues singers, they'll just throw in the occasional extra beat when they feel like, usually to fit the lyrics. I once heard folk guitarist Martin Carthy say that he considers a lot of his music to be in 1/1 time...i.e. just take it as it comes.
 
And then of course there's Frank Zappa. 

Indeedy!!!
 
 

"1/1 time"...I like that.
 
Funny how working within the constraints of a DAW's timeline trains you to think linearly. A group of musicians jamming don't ever think about what time signature they're in! Or often, even what key.