Is it normal for the peaks of an inverse of a track to be lower, or higher, than the original
No. A channel and an identical copy of that channel with polarity inverted should be absolutely identical to each other in every way except for polarity. That's why they should cancel out when summed to mono or both are panned to center.
But after converting M/S to L/R is would not be uncommon to have some content in one channel higher in level than the other.
I am using Wavelab and have the mid track sent to l/r and also l/r. The right side is sent to r and r, and the inverse is sent to l and l.
This is the part I don't follow and which others may not be understanding.
Given the way you are going about doing the Mid/Side to Left/Right conversion manually:
~Mid channel should routed to both the Left and Right output buss or panned to center.
~Side channel should be duplicated so as to populate two channel strips. Assuming that when making the recording you used the standard M/S setup with the front of the fig-8 (positive polarity lobe) facing Left, the original copy should be routed or hard panned fully Left. The polarity inverted copy channel should be routed or hard-panned fully Right.
~Mute the Mid channel. Adjust the channel gains of two Side channel copies so that they are identical. Mono or center-pan the two Side channels to confirm that they cancel each other. If they don't cancel, perhaps something other than a simple polarity inversion occurred when you copied them. Adjust the gain relationship between the two until they do cancel. Then lock the two Side channel faders together so that their relative gain relationship remains the same and both move together as a group.
~Unmute the Mid channel and adjust stereo width by the relative balance of the Mid channel against the pair-locked Side channels.
Could this just be due to bad aiming on my part?
If you are seeing that imbalance between Left and Right channels after doing the conversion, then it could be how the mic array was aimed, or it could reflect the Left/Right energy balance in the room from the recording position.