I know you're asking about PEI, but have you tried using Lipofectamine? I use that for my HEK293T transfections, and I've rarely had any issues.
If you're insistent on using PEI, what exactly are your experiment specifications (e.g. nucleic acid type, number of cells, etc)? Knowing a few more of those details might help me better to answer your question.
Only after number 1 should you proceed to optimizing transfection efficiency because mycoplasma contamination inhibits transfection (having experienced it myself). It is more common than thought.