What .exe are you using? I've had that problem with Carthage vs. Rome AI wars, but never with Seleukeia vs. Ptolemaioi. With BI.exe anyway, which is what I use, the bug seems to only come up when two factions go to war without having any territories they control adjacent to each other, making naval invasions between AI controlled factions difficult, if not impossible. I usually deal with this by manipulating the two parties into having adjacent territories somewhere.

I've heard that ALX.exe this sort of thing is pretty much fixed, but I haven't been able to get a copy of it yet. I didn't use RTW.exe very much before switching to BI, but as I recall it would do that sort of thing even if the factions were right next to each other. So aside from trying a different .exe you may be stuck with it.

You could try using the move_character cheat to banish their diplomats to the far corners of the earth, but that could easily get tedious, if not impossible, especially if you have to do it with factions who are right next to each other.