ARGH! Root cause: 4k sector size while harddrives report 512byte sectors. Misaligned partitions will cause severe performance penalties [0] and block IO in the process - causing VDR to lose frames.
Thank you very much, WD, wasted a lot of time and money on this sillyness. Re-aligning the partitions for the 4k boundaries fixes all performance issues. Just a heads up to others who might have missed this detail.
[0] http://en.wikipedia.org/wiki/Advanced_Format#Advanced_Format_512e :
The translation process is more complicated when writing data that is either not a multiple of 4K or not aligned to a 4K boundary. In these instances, the hard drive must read the entire 4,096-byte sector containing the targeted data into internal memory, integrate the new data into the previously existing data and then rewrite the entire 4,096-byte sector onto the disk media. This operation, known as read-modify-write (RMW), can require additional revolution of the magnetic disks, resulting in a perceptible performance impact to the system user.