Rick,
The OpenG Application Builder add-on (http://ogab.sourceforge.net) has a fix for this Windows bug. Unfortunately it is not upgraded for 6.1 yet. You can find a fix (still 6.0) at my labview page (http://cybertechs.qc.ca/~jpdrolet/labview) that you can rather easily port to 6.1 if you look at how it works.
Basically, the fix replaces a VI in the application builder LLB . The replacement VI calls the original VI (this VI makes the exe file) and then "touches" the maked executable file until the file dates are consistent.
Maybe the fix can be port without changes to 6.1 if the VIs names and connector panes didn,t changed. Then the only thing to do is to modify the installer so it allows installation on 6.1.