SPIDER relies heavily on a cache that automatically adjusts to available memory. If SPIDER runs slowly the best solution is therefore to increase the memory allocated to Eclipse, see for instance The Eclipse FAQ or search for "eclipse default memory" with your favorite search engine. Of course, the memory allocated to Eclipse should be well below the amount of physical RAM in the machine. Having a 64-bit Java (and OS) will help.
As a last resort it is possible to turn off the Indexer from the preferences. The need to turn off the indexer should be considered a bug in SPIDER so please report if you ever find it necessary to turn off the indexer.