I am having this same issue. After I close Boxee the process hangs in memory for up to 5 minutes and can not be killed via process or process tree. This sometimes causes trying to launch new apps, use something that requires the windows security launch dialog or maximize other windows to hang until boxee clears. The attached log is from this morning on Boxee's first launch after last nights reboot.
Time of this report: 4/24/2009, 10:01:34
Operating System: Windows Vista™ Home Premium (6.0, Build 6001) Service Pack 1 (6001.vistasp1_gdr.090302-1506)
Language: English (Regional Setting: English)
System Manufacturer: Acer
System Model: Aspire X1200
BIOS: )Phoenix - Award WorkstationBIOS v6.00PG
Processor: Athlon(tm) Dual Core Processor 4050e (2 CPUs), ~2.1GHz
Memory: 2814MB RAM
Page File: 1349MB used, 4508MB available
DirectX Version: DirectX 10
DX Setup Parameters: Not found
DxDiag Version: 6.00.6001.18000 32bit Unicode
Acer x1200 AMD dual-core, 3GB RAM, S.G. 1.5TB.
onBoard g.f. 8200 Vista 32bit home.