I'm using a pack (https://flipout69.deviantart.com/art/Kotak-foobar2000-icon-pack-404646366) of custom icons and the installer is replacing/restoring most of them, this didn't happen in previous installers, afaik.
Also, before, foobar used to detect changes on foobar2000\icons folder and trigger foobar2000 Shell Associations Updater.exe to update explorer.exe icons cache (i think), now it's necessary to kill and start explorer.exe to see custom icons.
No big issue tho.
Tested on Windows 7 (32 and 64 bits).
Peter seems to have somehow rewritten the icon files so their dates have changed. The installer overwrites icon files if the files in the installer are newer than your local copies. Touch the timestamps on your files after you replace them.
You're absolutely right, that fixed everything. :D