I have tested this on my FP-2015 and on my PC, and I don't have the behaviour you described. When probing offset values at the outputs of Seek and EOF VI's, I always read 512. Moreover, regarding the header, I don't use them, I store the raw binary data and read it accordingly.
If the problem came from this point why would I have a different behaviour when running the program on a PC and on the FP-2015 ?
Thanks in advance,
Gaël ROBIN.