Hey guys, glad you got it fixed. Typically when those issues happen there are 6 things to check.

1) Car Battery - Make sure voltage is up
2) Ground - Make sure the grounding cable is good, you can check by turning on the defrost with the ignition on, see what happens to other accessories.
3) ODBII Connector - These are starting to wear out in well used tuning vehicles. Loose connections cause bad flashes, Hondata has a thread on this somewhere.

With the Cal:

4) Accessories, like VSA, Secondary O2 etc, make sure are setup properly.
5) ROM Base - Different years require different base ROMs, ie 06 different then 07+. It could also be an AFM/MAP issue, different base ROM's again.
6) Bad Flash - Sometimes Flashes go bad, and then the ECU has trouble accepting a new flash as you found out. A total system reset followed by new flash seems to cure it, thanks Honda for engineering ECU recovery mode, better then a dual BIOS PC board

Hope that helps,

Steve