kernel : Add timer.running flag before enabling clk_ref_cnt

Make sure both increase and decrease of clk_ref_cnt are in sync.
If decrease operation is done when timer.running is true, then
increase the clk_ref_cnt when timer is true, otherwise both will
go out of sync when multiple threads are there.

Testcases :
1. Change verified by reporter.
2. Sanity testing done by APT team and all KM testcases passed.

Change-Id: I9676162d31848fcfa76e73e635d5185b6c861270
Signed-off-by: Sonal Aggarwal <quic_sonaagga@quicinc.com>