I'm sorry, this is confusing, you wrote previously:
We thought it would be easier to start by visualizing the results in a subset of the channels, so she created a 32-channel montage by selecting the electrodes of interest, using the same mastoid reference as before. She re-computed the statistics with the same procedure, except she used the process “apply montage” before the t-test.
This implies that the first test was performed using the original recordings, and the second one on re-reference data.
If indeed you tested exactly the same dataset processed exactly in the same way, the channels common to both cases should give you exactly the same uncorrected p-values, as each test is done independently. If they appear different, make sure this is not because of manipulation errors in one of the two, or simply because of differences in colormaps or other display-related configuration options.
If you can replicate this same observation, then there is maybe a bug somewhere. In that case, I would need an example dataset so I can reproduce the erroneous behavior on my end and fix the code accordingly. Please prepare one subject with only the test datasets, with four folders: trials of condition A 32 channels, condition B 32 chan, condition A 128 chan, condition B 128 chan. Keep the channel files and the minimum number of trials necessary to reproduce the error (two should be enough - just set the p-value threshold to 1 in order to see something).
Then right-click on the subject > File > Export subject, upload the zip file somewhere and post the download link here.