I too have started using MMultianalyzer.  It does a great job of displaying conflicts. I think the tricky part for most people is making the choices to resolve the conflict. That rolloff that sounds good in the mix can sound very thin if the other sound it was layered with drops out.  Sometimes a notch approach is better

hmmm...gate out some low noise or rumble..on each track...automation of volume at the marks of warble...panning to seperate...and momo to stereo...listening,...`Phasing issues ?.was this all recorded at once?..just some thoughts to get to a root...
Find the frequencies of each...try to cut the low end of the guitar...and leave the bass sit in the right low end, but use volume automation ....not sure about side chaining volumes..but i am sure the issue is not impossible to find the reason...once that is found,,,bliss comes....wink.

Oh ...making MP3s can be tricky...I do not go to zero on my mixes to mp3 but go upto -3 but not beyond , and cut the high and low eq ends  a bit / tail ends.(stops odd harmonics.especially on low bit renders of 64 bit or lower)...and it has to be mixed for that right, to get it good sounding...

why not post a file so people can hear?

konradh
Is it a slow cycle, like a phasing or comb-filtering sound, or is it fast?
 
I'm guessing you know what beats sound like when two sounds are slightly out of tune, right?  That's another thought.
 
Can you solo two sounds and hear it?

It's a fast tremolo effect...   it was doing just fine in the mix, and then something happened to create this new twist... perhaps just adding compression to the bass was enough to do it, I just have to get some more free time to get in there and sort it out.  At some point you start to wonder if you're hearing things...  but there's no doubt it appears in the mp3, and back-tracking it is there subtly in the mix.  Thanks for the idea about tuning...  
I had a similar thing happen on a different song with drums and bass, and had to de-resonate the drums a bit in Superior Drummer to fix the problem. 

I'd suggest bypassing all of your Fx and re-enabling them one at a time until you get the problem again