The TOP programmer software uses PC's CPU to do the part of the write job. Moving arround window while writing will interrupt the write process. So, you'd better let it finished job before you moving the software window.
Hi escher, I just programmed an SST 39SF040 successfully. Make sure you have the latest TopWin program (v2.21). And as ZLM said, when it programs, don't do anything with your computer. SST chips program slowly, so please be a little patient.