I've seen many people on Amazon.com, Newegg, and many forums such as this one and the Linksysinfo forums complaining about Build 54 not being stable with the RT-N16, either blaming the router as being "junk" or even blaming Tomato as being "unreliable".
Guys, it's an 11 month old build. You can't expect it to work perfectly on newer routers like the RT-N16 just because its "generally stable". Some bugs have yet to be worked out from specific routers.
I know many people here are FRIGHTENED TO DEATH of using something that is not an official stable build but seriously, it is illogical for you to continue trying to fix 11 month old code that clearly doesn't work with your router that well.
If you have problems with the RT-N16, you simply must upgrade to Toastman's builds, which are working fine for people, partially because Toastman himself personally uses an RT-N16 and depends on it to work flawlessly.
Enough with the complaints and start using newer code, ok? Clear NVRAM before and after you upgrade!