Is there any update on this issue? I also use a harmony remote and can confirm pressing the OK button when the "skip commercial" dialog box pops up does not work. The work around is to press the "skip" button I've programmed on the remote.
Along the same lines, can I suggest you fix the interface to still show the timeline when the "skip commercial" dialogue box appears. Since there are times when the commercial skip feature miss-calculates you could be skipping way too far if you select "skip commercial". If the timeline were visible you would know if it's OK to select it.