Ive notice it on FMH10 and also on FMH11 that once a transfer window shuts within a few days i normaly get a player injury for quite a lenthy time.
for instance my recent save with Roma i had J.A Riise out for 7 months, again just a days after the window shut in september

Had the same issue for van persie in my Arsenal game so dont think it is local to one set league.

Anybody else had this issue?