BIRB made color subtitles correctly. YouTube does not read them correctly. A simple SRT > SMI conversion fixes this.
1. Download BIRB's .SRTs on the forums, starting from Episode 54.
2. Manually save each .SRT as an .SMI (with a program such as "Subtitle Edit")
3. Upload to YouTube
The end
Confusing long version:
After explaining this to BIRB, they started uploading SMIs. You'd think that'd be good, except they're COLORLESS, entirely wasting the SMI format. Therefore, I did the conversion myself for Episodes 1-53, and uploaded on Captionfy, purely to demonstrate their full features. I and Captionfy are UNNECESSARY. All you need is to convert BIRB's SRTs to SMIs. So whatever you do, don't use BIRB's SMIs, SBVs, RARs, or any other files.
tl;dr:
BIRB's .SRTs > "Save As" .SMI > Upload to YouTube