I haven't used the synscan handsets so I had to do some reading up on this - hope I've got it right
In the user manual for the EQ5 synscan handset , under the section titled "Display Polaris Position" it gives
“Polaris Position in P.Scope = HH:MM”.
Where the HH:MM is the current position of Polaris set against an imaginary 12-hour clockface coinciding with the "large circle" in the Polarscope field of view. I assume that 12-o'clock is at the top of the field of view and the "hours" go round clockwise from 1 to 11. Each gap between the hours in the hour circle becomes 0-60 minutes (not 5 minutes as in a real clock) so it is probably quite difficult to place Polaris with better than 5 minutes accuracy.
In that case a Polaris position in the P. Scope of 12:30 would be halfway between 12 o'clock and 1 o'clock. A P. Scope position 06:45 would be three-quarters the way from 6 o'clock to 7 o'clock. These positions are what the handset refers to as "The hour-angle of Polaris", and it reads the value back to you when you confirm that you have aligned the mounting to that position (press Enter). Of course, before you press Enter, you will need to use the altitude and azimuth screws on the mounting to place Polaris at the correct position in the polarscope field of view.
From there the handset can use the star alignment steps to calculate corrections in software for any small errors in the polar alignment.
Just a couple of pointers I picked up elsewhere. Firstly make sure the mounting base is as level as possible - maybe use a small spirit level to check. Don't rely on the small circular level that may be built into the base. Secondly make sure you have a sufficiently reliable power supply to the mounting. Batteries can run down and low power can result in the goto problems you have described.
Hope I got it right and this maybe helps you a little,