I've had a VDS for probably over a year now and really like it. The TF2 and L4D2 servers work great. I also run a web site with apache (the server is on ubuntu) and the HTTP works fine but the HTTPS is something I've always had problems with and have never really been able to figure out.
Basically, when HTTPS hasn't been used in a while (or so that is my impression) it goes to sleep and the first time a browser such as chrome tries to access it, it times out. After that, if you refresh it works.
I've tried setting up a cron job to "keep it awake" so to speak but that doesn't seem to work reliably. I realize that hosting an SSL web site isn't the main point of these VDS servers but I just thought I'd throw this out there and see if anyone has any ideas of what I could try.
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What webhosting software are you running (is it Apache)? What shows in the log for the software, and in the system log, when you are retrieving the page and it is timing out?