Think I've tracked down the cause of the translucency problems - $5/€5/¥5/£5 says that the maps you're noticing it on aren't vissed for translucent water. There's some contents transition code I have (basically add visibility for the previous viewleaf if the contents are different from the current viewleaf) which isn't playing nice there. I'm going to remove that code anyway as it occurs to me that while it might work with the world, it won't with entities.
=peg= - I think you may be on to something with the map name. I'll need to review the code, but I have a feeling that I may have made certain assumptions about map names (and the level name in Worldspawn) which don't necessarily apply in all cases. Protocol limits shouldn't be an issue - this can load and run warpc, and has higher capacity than the Warpspasm engines.
Chip - morphing on weapons? Two things spring to mind - I have a low floating point precision flag set in my shaders, which is causing it, or the fact that - I think - I've mainly been using a "fixed" set of weapon models means I haven't noticed. Silly question - you're not underwater when this is happening, are you?
Still not certain about the ammo boxes, by the way. I think it looks good too, but it's a change from regular Quake. I believe based on Carmack interviews I've read that it's a change ID themselves would have considered desirable, and even that they would have considered the default handling of them as a bug. Not all change is bad of course, but this is one that probably needs a cvar to select it.