I am using the latest version of Mekanism.

I've noticed that every time I reboot the server I need to fly up to the salination controller and click the 'salination plant' button. Until I do this the controller reads as incomplete.

I'm not sure why it's happening but it's gumming up my 5x processing setup.

Confirmed! In v8, salin- err, solar evaporation plants will auto-assemble!

They seem to be fragile. I have to click that button every time I come back from the nether, or even sometimes after taking a long trip away from my base. Would be nice if they would auto-assemble after the first time.

It should only disassemble and reassemble when it detects a block update.

Right.

If you need an example of a robust multiblock, look at BigReactors.

This can no longer occur in the changes that come with v8.