Hatch is a weird tool. It helps to have all of your selected regions on the screen at one time.
Also, avoid entering extraneous commands while the hatch window is open, such as ortho, opening snap dialogue, etc.
If those don't work, you know, use the EX, TR, or F:R:0 commands to tighten up your regions, and kind of check...it's sometimes surpring how those snaps disappear at the most inopportune moments.
I've found that not having a dialogue box in the middle of your region helps, too.