Hmmmm ... I don't see the problem you are describing in TS12 ... all three work basically the same way from a numbering perspective ... here is the dependency list that I have ... check the versions of those dependencies that my copy is using ... maybe it will help run down your problem. Also, have you downloaded the TS12 specific dependencies from Jointed Rail? I have and I don't have the problem ... so ... it's something you might consider doing as well.
Ditchlight,<kuid2:45324:10100:3>
ES44DC engine,<kuid2:45324:6441:2>
gen dd40 int,<kuid:-3:10085>
GEVO12 diesel engine sounds,<kuid2:45324:53005:2>
HiAd Gray UP,<kuid2:37581:7501:1>
Locomotive sound effects library v1.05,<kuid2:45324:54002:3>
Multi-number library for rolling stock, v2.02,<kuid2:104722:2501038:4>
Nathan K5HL,<kuid:37581:1012>