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Sounds like a very interesting problem.  The most direct way to get to the bottom of this is if you could make available two set of files that illustrate this discrepancy:

a) A set of files (eg, raw, PSD, any other intermediate files in your workflow) illustrating your previous procedure, along with the pixel count that you obtained; and,

b) Same as above, except for your new workflow.

My guess is that the size of all these files (in both pixel dimensions and MB) will exceed the limits set by the forum's uploading software, so, you probably should make them available using Dropbox (or equivalent), or via an FTP site.  If you don't want them to be seen publicly, just send me their location via a forum private message

I'll try to have a look at them late tonight.

Tom M