I had been working on a custom application and we’ve had many…..challenges.  At one point, we believed we had it beat but then another issue arose and there appeared to be no easy resolution save for review the applications code and making some changes and after some searching, I found the following Citrix support article http://support.citrix.com/article/ctx966450 which states:

Though it is a best practice to publish applications by their executable, there are certain applications (such as legacy DOS and custom applications) where publishing through a shortcut (.lnk file) is required to maintain proper functionality. 

Initially I thought “there’s no way this is going to work” but after some testing, publishing my custom application through a shortcut solved the issue we were having.  This doesn’t work each and every time, but if you’re having problems with a legacy or custom app, try publishing the application via a shortcut.