3rd party attempts at Time Machine compatibility have not gone well in my experience.
That's not good news. Is this recent experience, or a few years ago? Do you remember the Netatalk/NetAFP versions you'd have been on, then?
Looks like my NAS is running 2.2.5, the newest 2.2 branch release. Laptop rebuilt it's backup on that one on October 13th. Not sure if the 3.0 or 3.1 releases improve it, I got frustrated enough to walk away from the problem for a while, hence the USB drive on the Airport now.
Perhaps this has improved, as the 2.2 era is also when the project was nearly cancelled due to lack of funding. Netgear by way of the ReadyNAS was one of the only storage vendors funding it at the time. This has improved a little since then, though I still don't know if Synology helps at all. They were off on their own forked version when the issue came up back then.
Overall I'd still recommend Time Machine somewhere in the mix for the wife's laptop at least. It has saved me a few times from accidental deletes or saves quicker then recovery by something like Crashplan.