I too am having a similar problem switching from LE 1.1 to LE4 4.1.3-. Uninstall reinstall and got it to work. Now the click track stopped working and sometimes playback stops if you walk away and come back it stops. It seems to be very similar to others.

PreSonus walked me through setting up the In/Outs (VST COnnections) but now no click track. this is essential as I am sending tracks to my drummer and KB player.

System:

XP SP3
Core 2 2.44
4 GB Ram
750GB Drives

Very efficient and fast system. only 165MB ram at startup. Runs LE 1.1 without issue mostly. Once and a while you hit record and nothing happens but otherwise fine.