There seems to be no way to 'use' (right click) a clock on a block while running FE.
The Playerlogger over-rides this.
This means you cannot place a clock into an infusion setup in Thaumcraft.
It seems the only way around this is to disable the server FE? - not yet tried...
Would it be more useful to have shift-right click to use the clock or some similar way to bypass the over-ride?
From another article, I think you might be replacing the clock system anyway?

You can use a hopper to put the clock into the table XD

Ah! Superb idea, thanks for taking the time, I had still been stumped!

You can also deny fe.pl.wand. Though I'm considering shift-right click though.

As @luacs1998 stated, denying fe.pl.wand is the correct solution for this problem.
You could disable the playerlogger wand in general and enable it only for yourself when you need it:

/p group _OPS_ deny fe.pl.wand
/p user <name> allow fe.pl.wand

You could also make a scripted command to allow switching that wand permission easily.

I think that should take care of this problem.
If not, we will have to think of some alternatives.

Better still - I shall give it a try. Thanks both of you.