IR remote freezes

I installed atvflash for the first time today.  My dealer installed IR remote (Savant) will not control the atv.

The atv remote works fine but the atv unit itself is not physically located by any of the tv's.  The atv remote via an IR extender from another room wont work either.  This did work with the native atv software before the atvflash install, thus this is software issue with IR control.  I can't find any help in the forum via the search function to resolve this. 

I have done the un-pair/re-pair several times and restarted the atv multiple times too.  I ran the smart installer.

Any help appreciated.