I have converted my InDesign (CS4 on PC) novel to e-book format and produced a generated TOC, but when converting to Kindle, there are huge gaps between entries in the ebook's TOC. The links work fine, but I can't produce it as is - it would be extremely annoying to readers. Does anyone have experience with this?
Ah yes, InDesign, software's gift to the ebook publisher!
Save that ID file as epub -- you can do that, right? -- then open it open in Sigil and fix it with Sigil's excellent TOC tool. Takes some learning, but easiest in the long term. You can get the latest version at https://github.com/Sigil-Ebook/Sigil/releases.
(Don't trust KDP to publish a print edition. Don't trust CreateSpace to publish an ebook.)