@Andrew
Hi, I had the same problem.
I don't know exactly when my Alfred lost transparency, but it must be related to some of my preference changes.
After changing to a new created macOS user account, I open Alfred and found the transparency is normal.
Can Alfred team locate the problem and fix it? Maybe I need to change to a new macOS user to make my Alfred appearance normal.
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB