Thanks for getting back on this. Is it a C or C++ file that you see this on, or will it occur with any type of file? What is a "medium" file to you? A few hundred lines, a few thousand, tens of thousands, hundreds of thousands, millions? Which version of Sublime? Are you using any plugins in Sublime?
The reason I'm asking all this is, I'm on a windows 8.1 64 bit ultrabook (Lenovo yoga2 pro) with an ssd, 8 GB ram, and a core i7 processor, SublimeText 3 build 3062, no clang, but I do have mingw installed, Anti-virus running (avast). On this particular installation, I have Anaconda, Evernote, InsertDate, Keymaps, Markdown Preview, MarkdownEditing, PlainTasks, Predawn, Theme - Afterglow, Theme - Flatland, and Vintageous plugins installed. I generated a sublime-settings file that was 350k lines (copy and paste the default settings file into a new file multiple times), and pressed and held ctrl+s for more than 10 seconds and had no issue, so there may be something I'm missing in my set up.