So basically I have this relatively long stored procedure. The basic execution flow is that it SELECTS INTO
some data into temp tables declared with he #
This is the footprint of parameter-sniffing. See here for another discussion about it; SQL poor stored procedure execution plan performance - parameter sniffing
There are several possible fixes, including adding WITH RECOMPILE to your stored procedure which works about half the time.
The recommended fix for most situations (though it depends on the structure of your query and sproc) is to NOT use your parameters directly in your queries, but rather store them into local variables and then use those variables in your queries.