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 set as the primary monitor and it should resolve most of those issues:
I like to have one of my toggle switches on the side of the pen set to 'Pan canvas'. However if you simply set it to 'Pan' within the Cintiq settings it will not behave properly. You actually need to leave it to 'application defined' and then set this within SAI's options panel in order for it to work properly.
Another thing I'd be sure of is to leave the 'tip feel' centered. You can adjust these settings within SAI and change tip-feel per-brush, so you can have really hard brushes and really soft ones. Otherwise it tends to skew the SAI settings towards softer or harder ones, regardless of how you set them within SAI.
I have eraser set to the other pen switch. This lets me very quickly erase something without flipping the whole pen around. A lot of people have this set up as right-click, but on the canvas this just acts as an eyedropper tool, which I can do from Alt-clicking with the brush out. You do need to right-click to set certain colors in the swatch editor, or to re-name pen tools. But you need the keyboard for this anyway, so I just use my mouse. It's rare that you need a right-click in SAI during your regular workflow.
These keys might be different on the larger Cintiq but I believe they're similar. I'm right-handed, so the left-hand side has my 'most important' tools. The right side has tools I use less requently and would have to pick up my pen to use anyway. I tend to 'undo' far more frequently than 'redo', so redo is on the right side. Also note that in the touch-strips, you can't actually set it to 'zoom' and 'rotate', you need to manually assign keystrokes. I'll list the shortcuts I'm using.
Undo: Ctrl + Z
Redo: Ctrl + Y
Brush Larger: ]
Brush Smaller: [
Alt: [Modifier] menu option, check 'Alt'
Fore/Background Color: X
Remove Frame: Tab
Flip Picture: h
The following are set as keystrokes within the touchstrips:
Zoom In: Page Up
Zoom Out: Page Down
Rotate CW: End
Rotate CCW: Delete
Tablet Driver / No Tablet Pressure:
SAI is picky and weird about it's drivers. If you have ever had two tablets installed on your computer, you will encounter this issue. Even if they're not plugged in at the same time. See, most programs choose the 'active tablet' to take instructions from. SAI just looks for the first tablet driver it can find and then ignores any others. So if you once had a Bamboo and you've just upgraded to a Cintiq, it will often find the Bamboo drivers first and ignore the Cintiq drivers.
You need to uninstall both, and make sure they're both removed, and then install the Cintiq drivers. If this does not work, there might be an errant driver kicking around that SAI is still finding. Or SAI is maybe just being weird.
There is a work-around. With SAI not open, unplug the USB to your tablet. Then start up SAI. Once SAI is completely loaded, plug the tablet in. This should 'show' SAI that you want to use that tablet. This has solved the problem for a lot of people.
Let me know if there are other weird issues. I'm willing to at least poke around. I've been messing with this for awhile and while SAI has some quirks, once you get it working it becomes really natural to use.