My theory about this (which I can't prove but makes sense to me):
New data enters the system mostly around the current date. Over time a lot of data gets created but after it is entered it mostly isn't changed. The older data is mostly just read but not modified. Staying on the same system (QuickBooks Windows Desktop for instance) means that the data does not change. When you switch to another system (even QuickBooks Mac Desktop) every bit of the data is read in, modified, and written out to meet the needs of that platform/system.
If there were any errors anywhere along the way (including in the older system) these things are more likely to show up after all of the data has been "touched".
Running rebuild corrected the issue you saw. I'm hoping it stays corrected without taking away any additional time from your work.