I have had some issue recently with the server. It would not register me fireing weapons, would set off the cool down timers on my BOFFs, but not have anyy effect. This is NOT caused by an NPC hold/Freeze/ ability. My ship moves and manuvers fine, but it is as if there is a "server not responding" except that the server is recording everything. Often, my ship will get destroyed when this happens.
This is particularly irritating when trying to complete "Defense Contract", "Traeleus Repair", and "Salvage Dispute". When logging out, and logging back in, the issue is resloved, but comes at a terrible price. Often my ship is destroyed. In the case of the missions above, the storage tank/Sattellite is destoryed, or the progress bar for the stolen ship completely expires in the intervening time.

This was an occational problem in Season 2. The problem increased in frequency during Season 3, and has occured at least once a day for me since Season 4 started.
Comments
Try the tracert and nettest that in other threads people are talking about. Then post the results here for someone to take a look at. They might be able to see an issue with data loss or a weak link that is causing this. There is also a sticky on the forums about setting your start up programs and to bring some offline that waste space and anything running in the background while the game is playing.