You can apply pull-up resistors to the counter outputs to force their default state to be low or high (depending on your requirements). Take a look at the following KnowledgeBase article (Default State of Counter Output Lines on E Series Data Acquisition Devices). At the bottom, there is a link to another KB that describes how you can change the default power-up state of the DIO lines, and this also applies to the counters.
http://digital.ni.com/public.nsf/websearch/008995633E33E47486256B5F00034436?OpenDocument
David McClelland
National Instruments