Problems in Capture: Color Documents and Page Order

We have had a number of problems with Capture and are curious about whether
other people have also had these problems or know anything about them:
First of all, the accuracy with which Capture performed OCR drastically
decreased recently. It's not with all documents; only color. Around the time
that it happened, there were several changes: a new computer, new software...but
all of these things happened at least a couple weeks before OCR stopped working
for color documents, and it was not a gradual process; one day, the OCR was
working fine, and the next, color documents were not searchable. It seems like
Capture is turning the text zones that I set up into image zones.
Second problem: After documents go through our workflow (or even just "send
PDF/TIF to file"), Capture spits the pages out backwards (first page last,
etc.). When the pages go through the workflow/OCR process, they appear in the
correct order, but in the saved PDF, they are backwards. This started happening
around the time that we hooked up a new scanner (a Fujitsu fi-5750C) and were
testing new software, namely ABBYY and Omnipage.
Thinking that these new programs could have affected Capture's performance, we
uninstalled the trial versions of ABBYY and Omnipage. The problems persist.
If anyone knows anything about these issues or has experienced them, your input
would be greatly appreciated!

The sequence issue is known to occur with various scanner models, probably a
miscommunication between Capture and the scanner driver. Check if you have an
alternate driver that might work better with Capture.

Check the dpi of the color scans. If I recall correctly, Capture has a range it
handles, and image files outside that range will be left as image only. The
range may be different for color/gray vs black and white. With your new computer
and software, you may have inadvertently been setup for different parameters for
the color scans.