Unicorn creates items in database (transparent sync)

[JaapioNL]

I've found an interesting bug that might be the cause of other issues. (Items getting serialized to the wrong location and items sometimes not having a parent). Some items that are in buckets get put on disk as well as in the database. I believe that when transparent sync is on the items should never be put in the database. I've had more issues with Unicorn losing track of these items because the code was being run inside of a cachdisablers and eventdisablers (I've removed these now). The only things that are being used now are LanguageSwitcher, SecurityDisablers and BulkUpdateContext.

Here is my config:

Target Data Store
Defines how items are serialized, for example to disk using YAML format.

Serialization File System Data Store
Stores serialized items on disk using the SFS tree format, where each root is a separate tree.

Serialization formatter: YAML Serialization Formatter
Physical root path: D:\xyzxyzxyz\Repo\sitecore\src\Sitecore.Data\Unicorn\xyz-xyz-xyz
Total internal SFS trees: 1
Source Data Store
Defines how source data is read to compare with serialized data. Normally this is a Sitecore data store.

Sitecore Data Store
Reads and writes data from a Sitecore database.

Deserializer: UnicornDeserializer
Evaluator
The evaluator decides what to do when included items need updating, creation, or deletion.

Serialized as Master Evaluator
Treats the items that are serialized as the master copy, and any changes whether newer or older are synced into the source data. This allows for all merging to occur in source control, and is the default way Unicorn behaves.

Item comparer: ItemComparer

Sitecore version: 9.0.1
Unicorn version: 4.0.4

Also something weird, normally items are located in:
D:\xyzxyzxyz\Repo\sitecore\src\Sitecore.Data\Unicorn\xyz-xyz-xyz\master_xyz\xyzxyzxyz xyz xyz\Content\Product

But sometimes they get put directly under:
D:\xyzxyzxyz\Repo\sitecore\src\Sitecore.Data\Unicorn\xyz-xyz-xyz\master_xyz\