WinMerge 2011 Portable includes both 32-bit & 64-bit versions of WinMerge 2011, however due to a small typo, it only ever launches the 32-bit version, even on 64-bit Windows. I noticed this when I couldn't compare a large file because it required too much RAM for the 32-bit version, and I was surprised by the error, since I was pretty sure the 64-bit version was included too.
I've tested the fix, and commited it to the AppConfigs repository (da1978272490738df39533d7b03cd220535aae59) so that it can easily be included in the next release of WinMerge 2011 Portable.
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Goodcatch. If you haven't already, I'd recommend building this as Rev 2 and sending it to John for release.
This is fixed in today's release of WinMerge 2011 Portable 2011.7.444
~3D1T0R