Please consider the fact that I'm SUCH a beginner. I literally began with my EQ6-R just two months ago. However, several factors have helped me with these challenges so far in my journey. I share them not as someone who is presuming to 'teach,' but someone who is a "fellow beggar struggling to find bread."
a) Try Green Swamp Software's ASCOM server if you aren't already using it. To me, it has proven to be much more intuitive and understandable, if not more reliable.
b) With the mount parallel with the North Pole (I know not how this works for South Pole users; please forgive; remember I'm a beginner), make sure you have your scope's objective lense/open end/corrector plate pointing westward when you mount it parallel to the ground on top the mount. Then loosen the clutch and point it toward Polaris. Turn the mount on with the OTA pointing at Polaris.
b) Stop trying to do one, two, or three-star alignments all together. As for me personally, I would advocate that anyone who is having trouble with alignment in general start immediately using SharpCap pro for polar alignment - period. Once aligned (5 minutes tops?), power cycle the mount, check Green Swamp Server again and confirm connection with the software you use for pointing (for example, AstroPlanner) to make sure it connects well with the mount, then ask your pointing software to slew to the first clear target. Then "Platesolve with sync" in Sharpcap. (The time taken to read about how to install this - and watch youtube videos about gearing it up -- will pay off over and over again every night.) The first slew MIGHT be 1 degree (or 6 degrees?) off. But it's NEVER been off more than 1 or 2 or MAXIMUM 6 degrees off on the first slew - then once AstroPlanner (or your pointing software) slews and Sharpcap plate-solves and syncs, from then on, the rest of the night, both sides of the meridian, your pointing should be from then on within a decimal fraction of a degree accuracy every time. 0.1 degree correction, for example - max. One-star alignment is no longer needed. Period.
c) Then using Green Swamp server, click the button to go home and every single time, it will return home - again - pointing at polaris.
If your scope is giving you a different result, then obviously, I've misunderstood something because I'm a beginner. But this is where I am on the journey.
Now someone with much more experience than I please correct me in any spots where I need correction. Remember, I'm on a journey. : )