What is the sample clock source for both applications ?
The difference between a timecode reading application and a DAW is that the TC app will follow the incoming TC independently from a sample clock.
A DAW can jump to a TC position (or MTC or SPP or Serial P2) but after this jump it must release the incoming TC and follow the hardware sample clock delivered by the audio hardware. If for some reasons this clock does not run exactly at the same rate compared to the incoming TC clock then an offset will start to grow.
The idea behind this is : if your master application generate a MTC that is clocked to a different sample clock compared to the sample clock of the second application, then this second application will not be able to synchronize to the incoming MTC because of out of sync clock rates (as a side note for most DAWs and audio hardware cards clock rates cannot be adjusted in realtime, eventually some DAWs can resample to adapt incoming and output sample rates, but this is consuming CPU power and deteriorate sound quality).
To my knowledge, Nuendo cannot resample to follow an external TC, but he can follow it using an external synchronizer that will recreate a word clock slaved from the incoming TC. This mean as well that you’ll need in this case some audio hardware with a word clock input. Anyway this is a bad solution because MTC is far from being a jitter free solution and its delay is not exactly known. So there is no guaranty that your slave machine or software will be frame and even less sample aligned even if both sample clock frequencies are well matched.
A better solution would be to give the same sample clock to both audio hardware through a word clock common reference. And the best for a more precise synchronization would be to use something like Rewire (for internal connections) or Video ref + TC or VST system link (for external connections) where timings are well known, jitter free and compensated. The advantage of VST system link is that it does use an audio digital output for synchronizing, so that there is no need to make manual delay measurements and adjustments.