The colors of blinking objects is defined in the .ini file / preferences...Read the following from the knowledgebase:
http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/564980ee2abe7e8e86256afd006a6dc1?OpenDocument
If you want to have multiple different blinking colors you'll have to do the blinking by e.g. changing the color of the indicator back and forth using the a property node. Here is another useful text:
http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/53614f5a1e850acc86256ab800658557?OpenDocument
Mads