That MQ variation listing you tried isn't using combined shipping rules - it's using a listing "additional item" rule (I don't know what the official terminology is for that if there is any) Those in listing additional item rules do only apply to a single variation and an external flat combined shipping rule would be needed to make that work,
The combined shipping I think OP is talking about is either flat or calculated combined shipping for multiple listings containing different items like the two I tried.
Looking at those 2 again (the jacket is calculated PS while the pants are flat price for PM PFRE) I think I may see what went wrong there.
I don't know for sure because I never tried it, but I don't think one can mix Flat cost shipping items and calculated shipping items or even calculated shipping items that use different services in combined shipping rules.
One can specify either flat rate combined rules that add or subtract $x for each additional item shipping after the first item with the most expensive shipping cost, or a combined calculated rule that does not combine weights (no discount rule used for dimensional weight items the calc cant handle), or adds the weights together and uses the greater of the total weight or the largest dim weight with the listing specified calculated service, or does that but subtracts Z ounces for each additional item after the heaviest.
Pretty sure that may be it. I'm really not in the mood to try and mangle my listings to test the theory, but can go look for a couple of OP's listings that both use calculated shipping and the same service or both use flat rate shipping using the same service. The combined shipping rule flat or calculated (OP only indicated one rule) should work for one of those sets of two items if I'm right.
Wandering off to find OP listings...
Flat cost shipping items
https://www.ebay.com/itm/RUSSELL-TECH-FLEECE-PANTS-BLACK-WITH-GRAY/323417119205?nordt=true&orig_cvip...
and
https://www.ebay.com/itm/RUSSELL-TECH-FLEECE-PANTS-BLACK/323417120684?nordt=true&orig_cvip=true
are both flat rate shipping using PM PFRE's, and if a combined flat rate rule is in place should discount in the cart....
And they do. Instead of $8 ea they are $4 each for a total of $8 shipping. Combined Flat shipping rule works.
Calculated shipping items
https://www.ebay.com/itm/CARHARTT-MENS-LARGE-JACKET/323443467905?nordt=true&orig_cvip=true
shows $10.13 PS calculated shipping to me (PS 5lbs to zone 5)
and
https://www.ebay.com/itm/Mens-Full-Metal-Choppers-Gray-Hoodie-Sweatshirt-NEW-NO-TAGS/323443377467?no...
shows $8.35 PS calculated shipping to me (PS 2lbs to zone 5)
When I put those in the cart..... the Jacket shipping drops to $7.44, and the sweatshirt to $6.13 for total shipping of $13.57 (which is the rate for 6lbs to zone 5 - must be an "add weights and subtract X ounces rule)
So combined calculated rule is working.
Last experiment is to find two calculated items with different services like PM and PS and see if it fails as I expect:
Calculated shipping items using different services
https://www.ebay.com/itm/CARHARTT-MENS-LARGE-JACKET/323443467905?nordt=true&orig_cvip=true
shows $10.13 PS calculated shipping to me (PS 5lbs to zone 5)
https://www.ebay.com/itm/Harley-Davidson-110th-Anniversary-Mens-Large-T-Shirt-House-of-Harley-Milwau...
shows $5.35 FCP retail shipping to me (12oz to zone 5)
when tossed in the cart.....
no combined shipping occurs.
Whether that is because I'm right that different services can't be combined, or because the PS shipped jacket is commercial rates while the FCP shipped sweatshirt is retail rates I do not know (how OP is offering both commercial and retail rates at the same time baffles me.) OP has no calculated priority shipped items I could find, so that's about all I can check.
In summary, the combined shipping rules are working - both the combined flat rate and the combined calculated.
The problem appears to be that flat and calculated shipped items can not be combined, and calculated items using different calculated services (like Parcel Select and First Class Package) can not be combined. Likely that OP's buyers were trying to mix items with those different characteristcs and that's why it failed.
One last thought on the combining of calculated items and flat items: it's borderline possible that they might be combinable but it isn't working because most likely OP didn't enter weight and dimensions in the listing for the flat price shipping items, and the calculator wants to use combined weight rules. Just wild speculation (may be that flat and calculated don't combine period)
