Check Tracker is missing a location

- [x] I have checked the known issues and searched Github to ensure this issue has not already been reported.
- [x] This is not a feature request, I know those belong on Discord/Github Discussions.

### Description of the bug:
Check Tracker is missing a location in Rando or the Randomizer is poofing on a location.

### Can you reproduce? If so please list the steps:
- [ ] No, I cannot reproduce this bug
- [x] Yes, here are the steps to reproduce the bug:
Play a randomized seed and watch as getting every check in every world according to the check tracker still leaves you missing a collectible.

### Expected behavior:
Check Tracker should have every collectible location.

### Screenshots or videos:

As you can see I only have 99 Jiggies but every world has all locations in the tracker collected.

### System Information:
- OS: Win 11
- GFX Backend: DirectX
- Game Version: 1.0.3
- Rom Version: 1.0U

### Additional Information:

[file3.json](https://github.com/user-attachments/files/30907990/file3.json)

Start with the Check Tracker and Rando/Randomizer behavior using the attached file3.json and the reported 1.0U seed context. Compare the tracker’s collected locations with the collectible count, then reproduce the run until the missing location is identified; done means every collectible location is represented and the reported 99-Jiggies case is resolved.

Written by the indexing model from the issue text.