This is a rarely seen and unconfirmed problem that you are seeing with the Timer function. I have posted some information as well as another Developer Exchange user posting a workaround at the following link that you should take a look at:
http://exchange.ni.com/servlet/ProcessRequest?RHIVEID=101&RPAGEID=135&HExpertOnly=&HFORCEKWTID=11348:5&HOID=506500000008000000AE1F0000