I rechecked the Decoy Mission in P3R-636 that you said was timing out for you. Starting at the Beta Site and running my ship's engines at 75%, I made it to the Stargate to P3R-636 with 30 seconds extra to spare before the job times out. I think the problem you may have is running your ships engines at around 50 to 75%. You shouldn't carry more cargo than your ship will allow so as to keep your engine speed at 100%. I mean I can add to the time on this mission but it may throw off the timing and make other players wait a long time for it to trigger. I can always add a few extra days though and shouldn't be too much of a problem.
As far as the Defending Earth/SGC HQ Spacestation mission you mentioned, I checked this as well and everything works out fine. After destroying all the enemy vessels you will receive an in-game meesage check the attachment below to see what it says. You will return to the SGC HQ Spacestaiton, if all enemy vessels are destroyed. The mission box that says in progress to defend earth and SGGC HQ Spacestation are just a reminder to defend both of these objects not just 1 and will disappear from in progress to completed one you enter the site center at the SGC HQ Spacestation.
If you do not get the in-game message I have below in the attachment then there must be an enemy vessel alive. Check the system and destroy all enemies including the Goa'uld Deathgliders. It is good practice to clear a system if a combat mission that is critical to complete (must not fail type) is not showing completed.
Keep me posted.
Re: Stargate SGC Conflicts In Space Star Fury Mod is now available for download
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