The Windows operating system in its 32-bit variant is constrained to 2Gb, I believe. However, if you are using a 64-bit version of Windows follow the instructions found here:
http://www.softwaresecretweapons.com/jspwiki/running_mysql_on_windows_with_4_gb_of_ram
This will almost certainly address your issues.
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Using lots of memory with MySQL
The Windows operating system in its 32-bit variant is constrained to 2Gb, I believe. However, if you are using a 64-bit version of Windows follow the instructions found here:
http://www.softwaresecretweapons.com/jspwiki/running_mysql_on_windows_with_4_gb_of_ram
This will almost certainly address your issues.