I'm not sure if this will help, but I have had a similar problem with an old computer with other games/programs. I tracked it down to some virus scan process being run like clockwork every 30 seconds.
Open the Windows task manager. Under the processes tab, sort by CPU (you may need to add these columns if they are not there already). As you play, watch it like a hawk for what processes are popping up at the top rows. You can also sort by CPU time to help find it. If it's frequently running, it's bound to accumulate CPU time and slowly make it's way top the top rows. I've also tracked some laggy processes to lots of disk reads/writes and these are also columns that you can add to the task manager list. There's also a resource monitor screen you can use in task manager that might help.
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