Flatten and merge is deleting random audio regions Logic 9

[Vertikoli]

So this problem has me tearing my hair out and I was wondering if anyone else is having this issue:

I have ten drum tracks (ungrouped) that I would like to flatten and merge after swipe comping, I want to do this as I really need the space and I am confident I will not need to revisit the comps in future. After flattening and merging all ten tracks I noticed that random regions of audio (guitar) on other tracks had disappeared completely. Thankfully I had the full project backed up on a drive, so I reloaded it back onto my laptop. As far as I could tell no other audio or MIDI tracks were missing.

There seems to be no pattern with this problem, it happens with various folders and audio tracks across several files.

The other issue I've come across with flatten and merge is the following error message which only appears when trying to flatten and merge a comp, not when using the glue tool:

"Merging take folders is not possible. Please flatten the take folders before merging."

After this error message appears, I click OK and audio from another random region disappears and all I am left with is a tiny white region of nothing. Apologies if that's not very clear, I forgot to get a screenshot.

Thought it might be worth noting that the latency button was off when not recording.

Here's what I'm using:

LP 9.1.7
Plugins: Waves, Kontact 5 player, Battery 3, Giant Piano, Massive plus numerous Logic stock plugins
Snow Leopard (all software up-to-date)
4GB ram
5400 RPM
Focusrite Saffire Pro40

All and any help very welcome!

[jim_branning]

well yoiu must be mixing up and trying to merge take folders as the warnings says

http://support.apple.com/kb/HT2889

you have studied this yes? partcularly this bit:

"If the new recording overlaps the existing recording by more than the count-in or pre-roll setting, a take folder is created that encompasses BOTH recordings."