MameDev FAQ. Basically, you changed mame version number, and something changed in what mame is looking for in the romsets that don't work anymore. For example, the neogeo bios has changed a few times recently, so neogeo games need the updated bios set to work.
And yes, the original roms on the boards haven't changed, but for it to never to change in mame's sets, they had to have been dumped completely and totally correctly and emulated perfectly the first time. Which doesn't always happen.
MAWS is a freat place to find what versions romsets have changed. For example, neogeo.zip set has
"
last change(s) .130u1 .128u6 .128u5 .127u6 .109 .092 .090u4 .090u3 .084u6 .081u4 .080u2 .080u1 .080 .079u2 .079 .075 .072 .071 .070 .068 .063 .062 .061 .060 .059 .056"
One of the most actively changed sets, though. Most sets don't change nearly as often, if at all. (And in fact, some of those changes were adding new bios versions, regions or languages, which you are able to get around without updating the set, but it's easier to update.)