[SCSI] bfa: Flash controller IOC pll init fixes.

Made changes to resume the flash controller if it is halted before going
ahead with flash controller pause/resume logic.
Made changes to avoid clearing off the interrupts during the initial
pll initialization.

Signed-off-by: Krishna Gudipati <kgudipat@brocade.com>
Signed-off-by: James Bottomley <JBottomley@Parallels.com>