Yes, that's what meant. He did a polar align (dovetail aligned E/W so you can use the polar scope), then put the telescope on the mount but left it in the E/W position when using the hand controller. That wouldn't explain it being pointed down at the ground, though.
There are two other possible solutions in an SGL thread from 2009 (see below). The first only applies if you installed your own GoTo kit on a non-GoTo mount and connected the RA and Dec cables the wrong way round. The second is possibly the most likely cause: a software issue. You may have the latest driver, but that doesn't mean the driver software is properly installed. It may not have downloaded correctly (data loss) and/or the memory section it's living in may be damaged. If a few bytes of code are corrupt or missing, the handset may appear to function properly but could get messed up when certain functions are run.