It could be anything. That's almost the database equivalent of asking "Why's my car making a strange noise?"

Probably you have some badly performing queries. Run profiler for a while and see what has high values for CPU and see if you can tune those queries. It may also be excessive compiles as by changing the indexes on that table, all query plans that use that table are now invalid and will have to be recompiled when the queries run. If that's the case, the cpu usage will drop off.