Acrobat 9 Pro: changed text in preflight

I just got an email from a client that there were some errors in the final printed piece. My InDesign file is fine. For some reason the printer wanted this catalog file as a PDFx1a. Usually for a PDF I export from InDesign and then preflight in Acrobat. I figured out that Acrobat preflight CHANGED at least two instances of text and I cannot figure out WHY. It changed "significant" to "signifi cart" -- added a space and made the "n" an "r." Also added a space to the word "align ment" -- which would almost be ironically funny if I wasn't so mad at this program right now.
Anyone seen anything like this before?!

I just did about 100 tests to try and recreate this. I did figure out the "n" in significant didn't change to an "r" -- it just got pushed up against the "t." It's all a spacing issue.
Here's what I have been able to figure out. The text in question is Helvetica Neue (TI) 8 pt on 10.5 pt. It has a paragraph style applied to it, but the font of 65 Medium was an override from the style. The problem occurs when this text is on the same page as a native .psd file with one layer and transparency. It seems that when the preflight does the step of "flatten transparency" the spacing in my text changes. I can't get this to happen by starting from scratch though. The other big problem is the client took the INDD file and worked on the copy separately on a PC in INDD CS3. I then got the file back and did layout on a Mac in INDD CS4. I can't help but think this is the problem, but why preflight would screw up spacing is beyond me.

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