Thanks for posting this and the wonderful replies. I just got my HEQ5 yesterday and I had a similar question. The zero on my reticule is also a little off from the home position on the RA axis.
On a related question, the manual says to power up the mount in the home position. Does that mean that I power it on to get the polar scope illuminated, do the polar alignment, then turn it off, put the RA axis into the home position, then power it back on?
I turned on the mount for the first time last night. I was able to use the same phone app to do the polar alignment and entered by location, time, etc. But when I went to do the three star alignment it was way off on the first star and pointed down at the driveway. I don't think that I paid much attention to the home position for the RA axis and telescope last night. I went back and checked my long., lat., date and time and they were all correct. Well, I'm going to try again tonight. Thanks in advance for any advice.