I have just been pretty successful at using TheSky for astrometry in a variety of setups, including imaging scales of 0.39"/pix.
I find this in TheSkyX manual which might be helpful..
"Check the All Sky Image Link Crop Options
For photos acquired with a camera that has more than 2500 pixels in one dimension, to speed searches, All Sky Image Link automatically crops the photo (see the All Sky Image Link Crop Settings under “Advanced Preferences” on page 226 to configure this option).If a photo acquired with a large format camera has few stars in it, or a very poor signal to noise ratio, the All Sky Image Link crop process can result in "not enough stars" being found.If your camera has more than 2500 pixels in either dimension, and All Sky Image Link fails, increase the default crop size to 80 percent or so and try All Sky Image Link again."
If you are by default using All Sky Image link, this could be the source of your problem. (If so, I presume you have downloaded the large sky database that TheSky uses for plate solving All Sky Image link images...) On the other hand, if your RA and DEC are approximately correct, and the OBJCTRA and OBJCTDEC keywords are being placed in your FITS header, then TheSky should default to normal ImageLink operation. That given, there are still a number of ways one can get foiled with astrometry, and it may make some sense to spend a bit of time solving your images manually with ImageLink to get the solve parameters right for your imaging setup.
If you would want to share one of your images, I would be happy to take a look at it.
Cheers, Ed Beshore