Space Port Esperanza mission series soft-locked after single-craft-multi-mission completion.

This is in JNO ver. 1.3.115 on Steam deck.

General description:
Using an SSTO carrying multiple SPE modules; upon completion of current missions and exit from the runtime, subsequent runtimes while carrying any module, single or multiple, will result in the immediate failure of the mission corresponding with the module present; this is on a module-instance basis, meaning for each mission, the failure is local. Upon re-acceptance of any module mission, the mission will no longer auto-fail, however, the mission sequencing breaks; it will only display the presence of the module and cannot be furthered upon, even if an attempt is done in the same manner as if the sequence was not broken (rendezvous, dock, then detach); this also breaks the built-in module deployers, which now only work if they are manually activated, and for those not able to be manually activated, the only way is to self-destruct the part.

Further details:
Using "/c/4W4lz7/Career-Reusable-SSTO" adapted for SPE modules. The payload consisted of 1 hydrolox tank, 4 command disks - each for the 4 modules: cupola, habitat, solar array x2, 4 monoprop tanks - each for each command disk, 4 multi-directional RCS for each monoprop tanks, 1 rocket engine, and 3 detachers - 2 on the side connecting the solar arrays group (1 mono tank + 4 RCS + 1 com. disk), and 1 connecting the cupola group. The habitat group has the connection to the hydrolox tank and the engine. The habitat group and cupola group are in series, with the cupola being outboard; the habitat group and the 2x solar array groups are in parallel. In the designer's staging editor, no payload deployment activation was present due to use of subassemblies, as the payload orbital maneuvering stage's stage performance analysis was impossible to be accounted for/seen, unless it was separately built. No staging editor node for module deployment presented itself even after deleting the part instance created from the subassembly and inserting a new instance from the add-part panel, while also changing the "auto" mission selection to the correct mission.
For the mission runtime, the launch was standard, rendezvous was standard, SSTO landing was standard. Docking occurred in this sequence: cupola, habitat, solar array, solar array. Note that there was only one mission for solar arrays, but I attached 2, because just one is weird. The mission sequence flow occurred normally and all 3 missions were successful. Also of note is that this mission did not increase the count of "unique docks", nor does any module docked to the SPE that corresponds to a bugged mission.
Afterwards, the mission series soft-locked as mentioned in the general description. At time of writing, I have docked, in order: 1 docking hub and 1 lab - single runtime; 1 habitat - using a different craft and just launching one module, this module mission was successful, although the mission display was still broken, and even thought it updated on dock, the deployment was still nonfunctional, and the destruction of the part was the only method; upon detachment, the mission updated to the deorbit stage, which upon adherence awarded the completion, this also awarded an addition count to "unique docks"; 1 habitat and 1 lab - single runtime, and 1 lab. I have also successfully rendezvoused 3 additional times with multiple mission modules without completion due to the aforementioned soft-lock, in which the impossibility of deployment - this was before the 2nd last runtime, hindered the mission, necessitating restart, as the design of the multi mission sequential deployment complex, was then requiring the low-impulse detachment of the built-in deployer; it was also built in a way that the previous module must detach to make space for the next module's docking.
Of the 2x single runtime-multi-module dockings, none were counted by "unique docks". All docks counted by "uniques dock" in the current "game" is as follows: 1 for droo orbit rescue, 1 for SPE com. pod and SPE expansion module, 1 for SPE and docking hub (nexus cross), 1 for SPE and habitat, first (saved) multi-module (null, but mission complete), 2nd (saved) multi-module (null, bugged missions), 1 for SPE and habitat, 3rd (saved) multi-module (null, bugged missions), 4th (saved) single-module (null, bugged missions), for 5 in total.
Single module runtimes now also do not work; using the same "different craft" and docking also no longer works.
Upon docking to the SPE, the staging will reset randomly to a stage that a bugged mission was previously assigned to (typically 3 or 4). Activating these stages does nothing. Even if the staging is finished to "end" and saved, upon each subsequent docking it will reset. It will also introduce empty stages, such as stage 8 (I think), where none of the craft docked to it had such a stage to begin with; the max stages of a craft docked to the SPE is 5.

I have yet to destroy the SPE to gauge a reaction.

The image shows the initial multi-mission payload, the one that itself was not broken, but may be the cause of the subsequent soft-lock.

I'm too lazy to get runtime screenshots.