I've had to help a few people with weird quirks between SAI and Wacom Tablets. Specifically with Cintiqs. I figured it would be good to list a few of the weird quirks I've found and their work-arounds somewhere, so I'm going to paste them here.
I find the line smoothing features worth some of the weirdness SAI has, even if I have to pull it into Photoshop later to add text or change things. 'Drawing' in SAI is really, really fluid and natural. I can't NOT use it now.
I have a Cintiq 12WX (the smaller one) and a second monitor. I'm going to assume you have a second monitor as well. If not, just skip that section.
SAI does strange things with tooltips if it's not set as the 'primary' monitor within the Cintiq calibration control panel. You'll try to pull down a drop-down menu and it will automatically close, or switch back to your second monitor when you click into SAI until you alt-tab directly into it. Just make sure SAI is s