When they release a film on a new medium (VHS, DVD, TV, etc.) they have to re-do the licensing all over again. In some cases, an agreement cannot be reached and so replacement music is used.
Remember when the 20th anniversary DVD versions of Breakfast Club and Sixteen Candles were released with "Original Theatrical Music" and people when ape5hit because the music was all wrong?
Meaning: the producers of the new DVD couldn't secure licenses for all the VHS music (the versions we all knew so well) so they used the music from the original theatrical run. Even if that was true, who the hell remembers what music they used in the theatrical version of Breakfast Club? Too funny.
So basically, that's what happened to In God We Tru$t. It's a failure to come to a licensing agreement.
In short: it's about money. Like everything else in life.