Meh, but its kind of hard to play netgames with JTE, since most people use the standard EXE. Thats why PrettySRB2 was created, to combine OGL fixes with an EXE that works with the standard SRB2WIN in netgames.
As far as what would make PrettySRB2 segment violate, who knows? I have had a few unexplained strange bugs just by using it normally, with no wads added. Personally I wouldn't worry about making your mod PrettySRB2 compatible, especially since by the time you figure out the reason, you could have had a dozen levels done, or more.