Played a little while last night. Still the boost settings screen has a few entries it either is not saving or reading so I expect eventually, there may be further issues on my system. Seams the longer I play the less entries it can read (a bit of guessing). Have not found the mod that conflicts, yet. Will keep checking. Only Idea I have right now is it might be a mod using either the same memory location or locking whatever routine that your app is using to access the file with the settings.
I do check daily for updates and new mods that look promising.
Maybe add a subroutine to your mod that generates an error message on the screen and a error log file when it fails to read a file with a code that tells you where the failure occurred. Just a thought. Might help identify why it is failing or which mod is locking your port to read the files. My specialty was Accounting and data access using Visual Basic and ODBC drivers, not games.
For now, Early in my new game, It is not reading the computer cost scaling for both Machines and Special Buildings sections. Though in the config.json file in the mod main directory they are set to zero. The game sets them in memory to default. 184 in machines section and 80 in the special buildings section. All else is set to max 1000 boost and 0 cost.
The Boost.txt file in the save game named folder in the boost folder has this.
55=995
54=1000
48=1000
97=1000
58=1000
60=1000
25=1000
23=1000
21=1000
75=1000
62=1000
29=1000
76=1000
34=1000
172=1000
173=1000
174=1000
178=1000
240=1000
migration_v1_done.txt
is set to 1
Transports.txt
137=10.000
My save game folder I am using at this moment is Warren4