The display quality settings normally do not affect the appareance of text. InDesign does have a "greeking" setting that could affect it, but that only pertains to specific sizes and display scenarios; I doubt that's what you're seeing.
The processing of a font's built-in hinting is an operating system function. If your system is overtaxed at a given moment, text may be temorarily distorted somewhat. Aside from that, I'd ask whether it's a particular font that exhibits the problem, or every font?