PADS will use the first decal it finds, so you may want change the order of your libraries:
Library Manager/Manage Lib. List.../Up-Down
As Chuck said, PADS choose the defined part decal in the first librairie it finds.
In this way,the solution should be to save your specific footprint in the first librairie as defined in 'librairie manager" or change the order of those libraire and put the one witch containt the right footprint in the first position (up/down)
A little beat complicated......
an other way,I would recommand to you, is the use of JEDEC Variation nomination.
You may have indenticals components or footprint saved in many librairies,but they need to be absolutly identicals if they use same names.
For my own I use JEDEC variations:
The original 7400 or DIP14 became 7400-AAA , DIP-AAA or 7400-AAB or DIP14-AAC and so on according to my needs.
I have already experiment troubles with using multiple librairies containing same part type with different footprint !
As Tom Hausherr (our commun Master) could say :"a good PCB laying began with a well organized librairies"(or something like that)
Have a good day/Bonne journée.