Many anti-Virus and mal-ware detectors just assume that portable applications, i.e. applications running directly from portable mass memory devices (for example a pen drive) are security threats and they simply block the portable application execution.
A trivial, yet inelegant solution, is simply to disable the Anti-virus or Mal-ware programs. Besides inelegant, this solution leaves the host system unprotected and most of the time, to disable the protection features is required admin privileges which the visitor,trying to run the portable application, normally does not have.
How do you cope with this? What is the elegant, effective and undisturbing solution to this general class of problem? 
Anyone´s help will be extremely appreciated. 
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No antivirus I've used assumes portable software is a threat. And no antivirus worth its salt should make such a poor assumption. Some corporate setups are set to block all apps from external media by choice, though.
Sometimes, the impossible can become possible, if you're awesome!
At times I become really upset with these Viruses