This is just my theory, I don't know if it's true, but it would predict just behavior I've observed
I've defined a custom syntax, with a custom .tmPreferences file specifying certain captured groups to both showInSymbolList and showInIndexedSymbolList.
However I realized while using it that if a symbol has only 2 characters, then even though it WILL show up in Ctrl+R, it will NOT show up in Ctrl+Shift+R, and that lengthening the symbol by 1 character (e.g. change it from "fn" to "fn1") makes all the difference!
I've used "show scope" and verified that both "fn" and "fn1" have the same scope. (Plus, they BOTH show up in GoTo Symbol; it's just that one shows up in the project-wide symbol list, the other doesn't)
This could be because I messed up somewhere else but before I investigate, I just want to ask a quick question first, whether this is indeed the case (that Sublime automatically exclude symbols from project-wide index if they are too short, less than 3 chars long)?
I've done some searches and nothing shows up.