Separating a combined midi track like you describe is not very easy.....
If I were to try this.... hummmm... I'd probably do it just the opposite of how you are doing it.
Let me splain this a bit.
First clone the track 2 times. This gives you 3 tracks that are exact. ( assuming you want to have 2 tracks at the end with 2 different instruments) Assign the tracks to the proper synths so they are playing the correct patch or sample you want.
Mute the first one and the third one.
Open the second one and let it start to play. Now.... like a sculptor.... carve away everything that isn't supposed to be there... delete the notes that are NOT supposed to be there.... this totally eliminates the need to copy, paste or move any notes. When you are done, the remaining notes should only be the ones for that particular instrument. If you delete a wrong note, simply use the edit>undo to put it back.
I have never used the PRV to edit midi, since I relate to the musical staff better I edit using the STAFF VIEW. It works the same but looks more like sheet music. Same rules apply. Delete the notes as you play through the time line. Move the start point along the time line as you complete a section on the screen. I would also recommend clicking the SAVE button from time to time. Since this is a time intensive operation, you don't want a windows glitch to blue screen on you and loose hours worth of tedious work.
When you complete the first track..... do the same to the second.... after muting the one you just finished. Work through it until you get the entire project worked out in this manner.
To me, it seems faster to delete notes than it is to do the copy paste and add... for the very reasons and problems you have encountered.
After you finish... unmute the two edited tracks and play them together. It should sound exactly like the original track, but you now have it split into two parts in different tracks.
Hope this was helpful to you.
post edited by Guitarhacker - 2011/12/11 18:17:33