I'm primarily logging this as a way to communicate to users an issue I've observed and the workaround for that issue. I've reported the underlying issue to Salesforce as it seems like a recent regression in the Tooling API and my hope is that they will address it in short order.
If you have custom classes in your org that aren't in your local filesystem -- typically from installed managed packages -- and you find that the OST isn't including representations of those custom classes, it may well be due to an issue where multiple parallel queries against the Tooling API for Apex class symbol table information is now returning empty symbol tables. IC defaults to parallel processing when generating OSTs because it dramatically speeds up the process. However, due to this recent regression, it seems to also result in a loss of data returned by Tooling API queries. The current workaround to this issue is to disable the Use Parallel Processing option for the connection against which you're generating an OST.
If this regression isn't resolved in short order, I'll add an option to use parallel processing for everything but this one step so that the issue is avoided but OST generation doesn't become fully serialized.