Ouch, my 808 just hurt me!

Okay, so I got a solid beat happening on Track 1, and a tambourine carry over for the fills on Track 2, Crash cym sound on Track 3. I thought last night I'll just merge 1 & 2 onto 4(D) and free up a track. Songs about 5min long, and I turned off Trk3 before I started bouncing. All was going fine till measure 40, then 'Drive Too Busy' comes up coutting out the sound.
Okay, I'll record from Measure 38 to 130 then. Fine up until Measure 56. Okay from 55 to 130, snap! Okay from 63 to 130, SNAP! 70 to 130, and so on. I eventually did the whole thing, and it worked out okay. Then I wanted to run the whole track through a Iso/Filt back to track A after I cleared the tracks 1&2 and did a Disk Cleanup - that was even more of a nightmare!

Anyone else go through this hassle? I wasn't even doing 'ninja' cuts with these beats hardly. Very straight and smooth measured loops and phrases.