I see two possibilities:
1. The SQL queries that BIDS Helper generate are very, very expensive (all the group by's and joins). So maybe you need to build some indexes or just be patient.
2. There are hundreds of thousands of problems that BIDS Helper is uncovering, and it's taking a tremendous amount of memory to build the HTML result table with the problem rows.
I would do the following:
a. run Profiler against the SQL database and monitor the SQL queries BIDS Helper is issuing. See if they are returning fairly quickly. If they are not, take a look at the plan and consider adding indexes or just being patient.
b. if the SQL queries are returning quickly, run them in SSMS and see how many rows are being returned. If lots of rows are being returned, then you have lots of problems, and possibly BIDS Helper is having trouble rendering that large number of problems.
c. check memory and CPU usage of BIDS. That might give you a clue whether it's problem 1 or 2. (High CPU or memory usage would suggest #2.)
please report back