It's probably the connection. Check your cables.
Thanks for the response but this is not the case.
I just tested with multiple external drives, different USB ports and different cables. In every case, the exported videos had glitches in them.
I still have no idea why this is happening.
I would assume, as Rick did, that this is a hardware issue. I've never heard of it before and tons of people render to external drives.
Just in case though, what happens if you install the 11.0.3 update to AE?
I installed the 11.0.3 update and the glitch is still there. Could it somehow be affected by the motherboard or something because as I said, it can't be the drives or connections themselves unless literally every drive, usb port and cable that I have decided to break overnight... How could I check the motheboard?
It seems I'm not alone in this either... found some people who had the same issue with external drives http://forums.creativecow.net/thread/2/996713 (near the bottom of the page)
I also had this problem and over here it had something to do with multiprocessing and quicktime. I render now in tiff-sequences and everything's fine now; or alternatively, rendering without multiprocessing.
I have had this problem on all external drives, both USB 3 & eSATA 3. I have never been able to render to an external drive.
Steve, if you want help with your issue, we'll need to know specifics about your system. Exact version number of AE (11.0.4, 18.104.22.168, etc.), OS, computer specs, etc.