This post is mainly to help ppl Googling related issues, as I have tried the lot to solve it, but these problems don't seem to be documented anywhere. For some years I have tried to use mate controllers with top level configurations and they seemed to work, for a short while, but are always broken on next use. I just moved from SW 2023 SP5 to 2025 SP 1.2, same issues still. But there IS a workaround that solves it... Scroll to THE ANSWER!

The first lesson here is don't use limit mates in mate controllers, they NEVER work as expected, for very long. Very prone to flipping orientation, and other general mess-making. So use set mates for the particular bits of interest, give them sensible names so you can find them, and a nice mate controller can be made. Not news, others have reported on this too.

Mate controllers work fine if they are in the top level assembly, where the behaviour is always as expected. Stop here, do not pass 'try harder', there is no joy there, I have learnt. Do not expect subassembly behaviour to reliably replicate in the main assembly either, even if driven by identical configurations in the main assembly - it will work when you are looking but break as soon as you are not!

The first 'suspicious' problem using a mate controller in a configuration is that the configurations won't 'stick'. I typically have 6 configurations, 4 are about positioning elements (eg Operational, Maintenance, Some Interim Condition 1 & 2) and 2 are overall configs (eg Skeleton and FEA). The mate controller is there to make equipment move to different orientations, mainly to demonstrate use cases of this equipment.

When things are good, the config list has a green tick in the active config and a grey tick in all the others. It may have warning or error symbols in any of these, telling you what to expect when that config is active. If you don't believe it, Ctrl Shift Q sorts the mess out (and many other flaky SW behaviours like phantom surfaces when graphics won't regen and Ctrl Shift B won't get them to either).

However, when you have a mate controller in the mix, only the last mate controller related config will stick, and any that are suppress only type configs, the rest drop to a grey dash, meaning they are not resolved. It is bad enough that SW already does this with simple non-relevant mods like renaming any item will blow all the grey ticks up so you lose staus of the configs. In changing configs requiring the mate controller to be active, you blow up any other configs and, often, the mate controller says it switched but, from the mate controller drop-down, it shows blank despite the tree showing a feature. And you have to switch it yourself. What a messy defective bit of software this whole section is. And frustrating waste of time, as there is a long period you think it is an operator error of some kind, because brief periods of seeming to work can be experienced...

THE ANSWER: Delete your mate controller and make mates for every condition you want, suitably labelled, and suppress or unsuppress them as you need. Put them in a folder if it helps. Yep, this is EXACTLY the job the mate controller is supposed to be doing, but do it manually and peace and good karma will flow in your space mouse again. All your configs will get their green / grey ticks, and keep them, no matter the combo of config switching you do! Hope this saves someone learning all this rubbish the hard way too... -:)