I had the same thing happen on a Windows XP machine updated to service pack three. It did the exact same thing, pause and then continue. On the XP machine, I booted in safe mode and deleted every driver that was installed and also deleted them from the hard drive. Rebooted in standard mode and re-installed the distribution drivers and now the machine runs fine.
I hate to hear your answer on the ASUS TF because I have a lot of data to be backed up and it is the time issue to backup, reset and all the time required to re-install the apps and set back up the data. When I first got the TF about 6 months ago, it had that pause and restart issue with HoneyComb. About the second update I did, corrected that issue and the unit has run fine from then on, until now that is. All that said, I know the hardware is fine, because of the amount of time I have used it. What ever gets busted with the ICS update should not of happened. ASUS should of taken more time to make sure. I have no apps installed other than the ones I have written. I have uninstalled them and done a hard power down reset and have the same issue. I don't know enough to know if Android accesses hardware with DMA or with Bios or the like, so if you know, can you explain why a factory reset is or should fix this issue. If it does correct the issue, it's because something is being changed. What? Another mistake ASUS has made is not given us the option to keep and rollback to the previous OS.