DV Info Net - Sony ClipBrowser 720/60P problems?

Can't find any hits on forums, google-at-large etc., so am now worried that I'm being a complete idiot.

Workflow: on location, use Clip Browser (V2.5) to copy all clips from cards to external HDD attached to laptop, then export to MXFs when I get back to base. All clips go into the same folder so that spanned clips get stitched together before export.

Problem is as follows:
Shooting 720/60P on EX1. Short clips no probs.
On clips over 13 - 14 minutes (or 4GB?), the camera (or more likely, clip browser) places an essence mark named "_ClipTransit-nn" (where nn is a two-digit number). This, I understand is normal (cards are FAT32).
When I export such files to "MXF for NLEs" (for input to Vegas), the audio gets messed up at that essence mark. It becomes an (approximately) one frame burst every second.
Export seems to ignore In and Out points - it exports the whole file anyway.
So as a workaround, I'm using the "New clip using in/out section" feature to chop the original clip at one(?) frame before and after each essence mark. Export then proceeds normally, but I lose one frame(? maybe more - still testing) every 13 - 14 minutes. I can export the entire clip to get all video frames, then export each sub-clip to get all but those odd frames per 13 - 14mins of audio, but this is time-consuming and tedious.

Apart from the sub-clip creation time and double export time, there's no way to position the cursor at an essence mark so you can mark the out point (or in point). The only way I've found to do this is to use the left and right arrow keys to scrub through the footage and wait for the "Delete essence mark" to become un-greyed momentarily, then step back one frame at a time until it stays un-grey. (And then it seems like the in- and out-points might automatically re-position at the nearest start-of-GOP???)

As I said earlier, I'm using Clip Browser is V2.5 (V2.05.000.246 latest update 2009-02-23. I installed this after I hit a problem with V2.0 where 720/60P audio was one frame per second throughout the entire clip...)
Clips are held on a 1.5TB external HDD (obviously NTFS, so no 4GB file limit issues there...)

This issue didn't occur with 1080i footage. There have been other reports of audio problems with 720P in clip browser, so I assume my problem is related.

So - questions:
1) Is this a problem between my chair and my keyboard (i.e. me)? If so, what am I doing wrong?
2) If not; is there a better workaround than the one I described?
3) If not; any idea how I report a possible bug to Sony? And what kind of response can I expect?