The skew you are seeing may be due to the trigger specification for 5112 synchronization. The system reference clock has a maximum skew rated at <1ns but the trigger skew specification is <10ns. If the skew you are seeing is between triggers, this may be the problem. The samples should still be synched if you are using the same system reference clock. If so, you could delete the extraneous samples off of the front of the waveform and then have a functional skew of <1ns.
The High Speed Digitizer user manual is linked below.
http://digital.ni.com/manuals.nsf/websearch/998C51E969F4900486256D9F007103F2?OpenDocument&node=132090_US
Hope this helps,
-Adam