You weren't using version 1.2.0 by chance, were you? It was the ROMless version, meaning you didn't have to have a Lisa ROM file in order to use the emulator (akin to Boycott Advance or PCSX-R's "simulate BIOS" function). Later versions appear to need the ROM file. Other than that, I'd say you're missing a file or two somewhere, but it's impossible to know because I wasn't using it on a PPC Mac then switching to an Intel Mac.
Also, the filesystem, core services, and frameworks got a major overhaul going from Panther to Tiger, and then again from Tiger to Leopard. It's entirely possible that your upgrade to a new OS also made using LisaEm impossible, or extremely frustrating.