For the games that aren't working, have these been tried by first installing the game to the Wii's NAND, running game, creating save (if necessary), saving in game and finally transferring the save contents to the emulated NAND, as was suggested is necessary for Bit.Trip.Core?
Also, do all of our Wii's contain the same files in shared1, or do these get added on an as-needed basis by the WAD's themselves?
For comparison, here's what's in my shared1. You can copy the contents to an .sfv file and verify against yours if interested. Unless it's a well-known fact that the contents are all the same and comparing is unnecessary, in which case, just ignore this.
CODE; Generated by QuickSFV v2.32 on 2009-10-13 at 21:07:51
;
http://www.QuickSFV.org
;
; 33608 22:31.22 2009-09-29 00000000.app
; 26128 22:31.22 2009-09-29 00000001.app
; 15352 22:31.22 2009-09-29 00000002.app
; 10664 22:31.22 2009-09-29 00000003.app
; 171800 22:31.22 2009-09-29 00000004.app
; 288140 22:31.22 2009-09-29 00000005.app
; 60776 22:31.20 2009-09-29 00000006.app
; 448600 22:31.20 2009-09-29 00000007.app
; 40976 22:31.20 2009-09-29 00000008.app
; 21776 22:31.20 2009-09-29 00000009.app
; 11776 22:31.18 2009-09-29 0000000a.app
; 353448 22:31.18 2009-09-29 0000000b.app
; 157996 22:31.18 2009-09-29 0000000c.app
; 33608 22:31.18 2009-09-29 0000000d.app
; 26152 22:31.18 2009-09-29 0000000e.app
; 15352 22:31.16 2009-09-29 0000000f.app
; 10664 22:31.20 2009-09-29 00000010.app
; 171900 22:31.16 2009-09-29 00000011.app
; 360460 22:31.16 2009-09-29 00000012.app
; 62484 22:31.14 2009-09-29 00000013.app
; 450296 22:31.16 2009-09-29 00000014.app
; 42572 22:31.14 2009-09-29 00000015.app
; 30584 22:31.14 2009-09-29 00000016.app
; 19092 22:31.14 2009-09-29 00000017.app
; 28404 22:31.12 2009-09-29 00000018.app
; 357068 22:31.14 2009-09-29 00000019.app
; 158564 22:31.12 2009-09-29 0000001a.app
; 158564 22:31.12 2009-09-29 0000001b.app
; 360428 22:31.12 2009-09-29 0000001c.app
; 158420 22:31.10 2009-09-29 0000001d.app
; 360108 22:31.10 2009-09-29 0000001e.app
; 27672 22:31.08 2009-09-29 0000001f.app
; 62568 22:31.08 2009-09-29 00000020.app
; 10800 22:31.08 2009-09-29 00000021.app
; 62752 22:31.08 2009-09-29 00000022.app
; 447724 22:31.08 2009-09-29 00000023.app
; 9356 22:31.08 2009-09-29 00000024.app
; 521008 22:31.06 2009-09-29 00000025.app
; 162064 22:31.04 2009-09-29 00000026.app
; 686468 22:31.02 2009-09-29 00000027.app
; 2156800 22:31.06 2009-09-29 00000028.app
; 370880 22:30.56 2009-09-29 00000029.app
; 4559887 22:31.00 2009-09-29 0000002a.app
; 2669044 22:30.38 2009-09-29 0000002b.app
; 3649020 22:30.24 2009-09-29 0000002c.app
; 10328143 22:30.54 2009-09-29 0000002d.app
; 1819808 22:30.06 2009-09-29 0000002e.app
; 1572320 22:30.04 2009-09-29 0000002f.app
; 272512 22:29.56 2009-09-29 00000030.app
; 606016 22:29.56 2009-09-29 00000031.app
; 53216 22:29.52 2009-09-29 00000032.app
; 70336 22:29.52 2009-09-29 00000033.app
; 112448 22:29.52 2009-09-29 00000034.app
; 1015434 22:29.54 2009-09-29 00000035.app
; 33520 22:29.50 2009-09-29 00000036.app
; 27796 22:29.50 2009-09-29 00000037.app
; 15352 22:29.50 2009-09-29 00000038.app
; 10800 22:29.50 2009-09-29 00000039.app
; 362376 22:29.50 2009-09-29 0000003a.app
; 62896 22:29.50 2009-09-29 0000003b.app
; 447868 22:29.48 2009-09-29 0000003c.app
; 521008 22:29.48 2009-09-29 0000003d.app
; 162744 22:29.46 2009-09-29 0000003e.app
; 26988 22:29.46 2009-09-29 0000003f.app
; 10800 22:29.46 2009-09-29 00000040.app
; 19428 22:29.46 2009-09-29 00000041.app
; 28472 22:29.46 2009-09-29 00000042.app
; 6208 22:29.46 2009-09-29 00000043.app
; 1904 22:29.46 2009-09-29 content.map
00000000.app 9A745D4A
00000001.app 112E32B7
00000002.app FFC38F0F
00000003.app B27E5510
00000004.app 7F4D7417
00000005.app B7DBC6F3
00000006.app 8D240B1F
00000007.app C480CE22
00000008.app 2648EFCE
00000009.app 29E97444
0000000a.app 51893841
0000000b.app 9F29E358
0000000c.app 1D7ED739
0000000d.app 403A4FEA
0000000e.app E681A841
0000000f.app 38A74D64
00000010.app CB5DD7C7
00000011.app E7022805
00000012.app 76904217
00000013.app 5FD12B42
00000014.app 107A3D20
00000015.app E13F0669
00000016.app 22D46D47
00000017.app 746B909E
00000018.app BBF4900B
00000019.app E70CDE63
0000001a.app 496973EC
0000001b.app 8A4360E0
0000001c.app F4B737DF
0000001d.app F35BA627
0000001e.app 769D453B
0000001f.app 331E8728
00000020.app C05D02CC
00000021.app 3B48B946
00000022.app A27FB5B4
00000023.app 87F0E286
00000024.app 1F161706
00000025.app 01A289F9
00000026.app 4054F7F2
00000027.app 37A9D6D4
00000028.app F56CF8EA
00000029.app DD09CBAC
0000002a.app 11988625
0000002b.app 95B89D45
0000002c.app 2D2F1111
0000002d.app D78900BC
0000002e.app C39100E4
0000002f.app DF21003B
00000030.app 2F732001
00000031.app 085B645F
00000032.app C9C919C6
00000033.app 99F952BC
00000034.app B2BDA882
00000035.app F481BEDC
00000036.app C42FFC4B
00000037.app 823F95B3
00000038.app 5DE46B88
00000039.app AAA7A85B
0000003a.app 6492A130
0000003b.app 09F6E055
0000003c.app 7A8762E5
0000003d.app AED0D623
0000003e.app 00B31294
0000003f.app 0B00C947
00000040.app 2DFF2CCC
00000041.app C147A80E
00000042.app D88B12E1
00000043.app 29406040
content.map 9A862A8E
That's from a 3.3U (v2 I believe) Wii.