You can't just tweak limits.conf to make your schedules work efficiently. This symptom usually means that you either have too many scheduled searches (reports, alerts, corellation searches) defined altogether or - more probably - you have them squished into the same "schedule spots" as @kkrises suggested. For example - you're trying to run all your searches at 5 minutes past the hour. It's the typical case and you should spread the execution times more evenly throughout the hour, day, or however often your searches run. In some cases you could try to run more searches at once but that's more tricky and requires more troubleshooting and diagnostics.
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