I just followed your process to the letter and had none of the problems...
The problem you're describing was happening a couple of builds ago in another area of MC; when in view schemes, say you had your view filtered by selecting a particular genre, then album. If you selected some random tracks in that album and changed the genre and refreshed the view, you would have the selections in exactly the same places, but with different files because the new-genre files were filtered out...
However, on my machine this behaviour is gone as well!
Media Center Registered 11.0.265 -- C:\Program Files\J River\Media Center 11\
Microsoft Windows XP Workstation 5.1 Service Pack 2 (Build 2600)
AMD Unknown 2207 MHz MMX / Memory: Total - 1048 MB, Free - 544 MB
Internet Explorer: 6.0.2900.2180 / ComCtl32.dll: 5.82 (xpsp_sp2_rtm.040803-2158) / Shlwapi.dll: 6.00.2900.2627 (xpsp_sp2_gdr.050309-1648) / Shell32.dll: 6.00.2900.2620 (xpsp_sp2_gdr.050225-1820) / wnaspi32.dll: 4.60 (1021) , ASPI for Win32 (95/NT) DLL, Copyright © 1989-1999 Adaptec, Inc. / Aspi32.sys: 4.60 (1021)
Ripping / Drive F: SAMSUNG CDRW/DVD SM-308B Mode:Normal Type:Auto Speed:Max
Digital playback: Yes / Use YADB: No / Get cover art: No / Calc replay gain: Yes / Copy volume: 32767
Eject after ripping: Yes / Play sound after ripping: No
Burning / Drive F: SAMSUNG CDRW/DVD SM-308B Addr: 1:0:0 Speed:2 MaxSpeed:8 BurnProof:No
Test mode: No / Eject after writing: Yes / Direct decoding: No / Write CD-Text: Yes
Use playback settings: No / Normalization: None