I do have two other mods Bailknights graphics and Real Capitial Ships (I like them being stronger) I do have the Double Research Mod enabled as well.
Yup, Bailknights was the problem with him to. You must have E4X above Bailknights or any other mod that might change default frigates in your mod order, otherwise they will not have their new E4X abilities. Sadly this will come at the cost of many ships not having the new weapons particles.
In theory it doesn't have to be this way, but bailknights was a pre-Rebellion mod, and Rebellion added lots of new particle effects and changed the names of all of them. This is a problem because bailknights mod had the particles named by their old names. I'm assuming you got that version of Bailknights from Ricks Galaxy, and while Rick was an awesome guy to update the mod, he did it by changing the ship files to use the old particle effects names, not changing the names of the particles themselves. While this likely saved him some time, it also causes problems like you have with mods that also try to change how those ships work.
*End technical rant*
In a nutshell, E4X and that version of Bailknights do not entirely work well with each other. If there was a version that worked flawlessly I would have included it in the official minimods. It will crudely work as long as E4X is above Bailknights in the mod order, but some ships will go back to using default weapons effects.
Real Capitalships should work better assuming it only changes capitalship files. The only capitalships I changed were the carriers to reduce the number of strikecraft they have as I made strikecraft stronger so I could make carriers more expensive, but I guess if you want stronger caps you won't really care about that. Hopefully you should be able to have Real Capitalships above E4X in your mod order without any noticeable issues. Though I imagine heroes seem less important with normal capitalships being stronger.