Just a while ago I started this thread:
http://forums.creativecow.net/thread/142/856755
I've talked to Sony a couple of times and they say there's a bug in the EX1's firmware. When using "clock" as timecode it messes the timecode up when writing to the cards. I was using 720/25p. Don't know what your timecode settings were...
My workaround was using a PC. Sony's ClipBrowser for PC can export MXF files. I downloaded a demo of Sony Vegas which can convert the MXF's to Uncompressed Quicktime MOV's.
Not the nicest way to do things, but I got the shots transfered (don't have SDI in).
I turned the setting back to "preset" and keep my fingers crossed...