Exports differing from timeline/weird stuff

Hi everyone.
A couple of weird little problems going on here that I thought you may have bumped into. We're running FCP 7, AJA Kona LHi cards for I/O, snow leopard.
It is an education institution technically so the machines do get a fair bit of use, but I've checked all usual sequence settings, trash prefs etc..
We're running into multiple problems: clips suddenly having time-code generator filters applied to them out of nowhere (not all clips in timeline), crossfades applied to almost all clips on the timeline (this couldn't be a user error selecting all and hitting command + T since some don't have fades even though there are handles) and most annoyingly, exports differing from the timeline. For instance, I applied a blur to a duplicate of a clip, matted it out to only affect a certain area of the clip. On export, there is a quick grey flash and then the brightness of the whole image drops for one frame. Doesn't do it in the timeline.
We're also experiencing tiny little zooms at the beginning and end of frames on some exports. We think we might have this one solved as it's only happening on footage shot on the Panasonic AG-AF101 which was transferred straight into ProRes without going natively to AVC first, which has resulted in some strange interlacing problems compared with 5D footage in the same timeline, also transcoded to the same ProRes settings. We rendered everything to ProRes LT then exported and this seems to have got rid of it.
ANYWAY, sorry for such a long post but I just wondered if anyone has seen stuff like this, bearing in mind that we're always working with the correct sequence settings with decent editing codecs (usuallly prores), and if anyone has any tips..
Cheers!
Kit

This is months later, I know, but I'm wondering if people are still having problems with this.
I'm shooting on the ag af-101 and transfering the folder in it's entirety to a hard drive, then logging and transfering into final cut 7. Pro res 422.
What I'm getting is, I think, what a previous contributor mentioned - a strange strobing or what I would call a juddering on some footage.
It seems to be on pans and reveals but also on movement of characters within a motionless frame.
It's possible it has something to do with the camera but it seems more likely to be a final cut issue.
Any thoughts?

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