Thanks for the screenshot it helps a lot!
Is this your color?

If it is, try running "Find & Replace" to replace all instances of #AAAAAAFF with #FFFFFF.
Here's what I think is happening...
VLC can read basic HTML attributes <b> for bold text, <u> for underlined text, <font color=#hexValueCode> hard-coded subtitle text</font>. Sounds like Premiere is adding in a couple extra characters (usually hexValues for colors are 6 characters, not 8) to allow Transparent Text.
VLC is only reading the last 6 characters, so it thinks you want purple subtitles instead of white ones.