Different outputs of computeMatrix depending on binsize
Please don't send things like this to the deepTools mailing list and post them here.

As I mentioned on the list, what you're likely being surprised by is that computeMatrix is not summing values, but taking the average in each bin. You can change this with the --averageTypeBins option (the default is mean, you presumably want sum).

Update: For those wondering the cause of the confusion was due to not using --missingDataAsZero. In other words, including or not including NAs will lead to different results, since different numbers of values will be included.