With multiple servers and problems, references like “this server”, “the error” and “this problem” are confusing. If you’re talking about “uploading from the wrong directories”, after exclude was added:
In the special case that all rules are include rules (which does not make sense when all files and folders are included per default) Duplicati assumes that all other files and folders are meant to be excluded (this had to be defined as another rule in Duplicati 1.3 but most people found that confusing so we changed that in Duplicati 2.0).
might be the explanation, but it would depend on what’s checked on the source tree. If it’s C:\Users\ shown on the later screenshot (is this the same system that used to have Exclude?), it’s more likely.
My guess is that the goal is to include certain desired folders from user profiles, ignoring any others, however cache exclude caused the “special case” above to end, so all of C:\Users\ flowed right in…
The TEST-FILTERS command can be used to explore filters. I’m not an expert, but find it confusing.
EDIT:
For tests, it’s probably worth setting up an example structure with many fewer files, like this (or half):
C:\tmp\Users>tree /f
Folder PATH listing for volume Windows
Volume serial number is ###-####
C:.
├───User1
│ ├───Documents
│ │ │ document.txt
│ │ │
│ │ └───documents subfolder
│ │ document.txt
│ │
│ └───Downloads
│ download.txt
│
└───User2
├───Documents
│ │ document.txt
│ │
│ └───documents subfolder
│ document.txt
│
└───Downloads
download.txt
C:\tmp\Users>
One thing to be careful of is subfolders. I’d assume the intent is (for example) Documents and below.