Hee hee... I actually know the answer to this one...
I had this problem when I exceeded the maximum number of entries in ships.tbl. By default, FS2 supports 130. You put in 131, and it screws up the player entry delay. You guys can dispute this if you want, but I have isolated the cause of the problem down to exactly this... course, that was for my settings. Perhaps a different problem is mucking up your game, Sid, but I'd try experimenting with the tbls.
Out of interest... anyone know if the SCP boys raise the maximum number of tbl entries as well, or just the file size limit?