Remote Buddy should only re-generate its entry in your login items (and re-launch subsequently) when you've checked the "hidden" checkbox of its entry, because - if that option is checked - it will prevent Remote Buddy's menu from appearing.

Regarding startup time:

Actually, Remote Buddy has recently gotten a lot faster during start up, because it now skips the most time intensive part for those of its 100+ Behaviour plugins that aren't needed on a particular system - which is loading them in full.

Please keep in mind that, when you are launching many applications on startup, all of them will launch at once and try to get their application's data from different parts of your HD, causing it to seek around a lot. Seeking a lot, however, will make even the fastest HD crawl. That's also the reason why applications launch much, much faster on SSD-equipped systems: there's no magnetic read/write head that needs to reposition and wait until the platter rotates to the point where the head can read the wanted data from it (which can quickly add up).

Keeping that in mind, chances are that, when you last updated your copy of Plex, Remote Buddy - or any other app you launch at login time, OS X stored their data at a greater distance from each other, increasing the impact of seeking.

Best regards, 
Felix Schwarz