What is the cause of this voltage difference between my breaker panel and AC unit?
Conduit is a perfectly acceptable grounding path
EMT conduit is a valid grounding method.  I would be surprised to see a ground wire inside EMT - nothing wrong with it, just would be &quot;belt AND suspenders&quot;.
However, it may be appropriate if you are in weather conditions where the EMT is rusting - it's possible for the clamps/bonds to rust out and give you a poor grounding path.  You can go with green stranded wire (which is easier to pull) or bare solid wire (which is harder to pull, and will make future pulls harder, but is better under &quot;conduit fill rules&quot;.)
When I say &quot;pulling&quot; I mean most people run a stiff &quot;fishing tape&quot; down and use it to pull a wire through.  I usually don't bother, or don't want to push my metal tape into something hot.  So I just push the wire down the conduit and  do a whole lot of coaxing and sometimes a little light disassembly of a conduit joint. Intermediate access points are very helpful, e.g. that junction box you mentioned.
Since you disconnected the conduit from the A/C unit, you have broken the grounding path if it was good before. If you had a ground fault, it would be &quot;pulling the chassis toward one pole or the other&quot; and the two hot-chassis measurements would total ~240V.  However since it is not, and they are equal, I would say you are detecting the weakness of your grounding path.
I would not tolerate that for a minute; disassemble and wire-brush it as much as you can, and consider running that ground wire.  #10 should suffice for all circuits, and hardware stores sell bare #8 solid.    I would use green stranded #10.
You can also replace rusted sections of the conduit, but that requires pulling the wires out.