Reinstalling the system menu WAD will overwrite Priiloader, so you need to proceed carefully. If you mess up, you won't have Priiloader to save you. Installing Priiloader is unlikely to cause this kind of problem. What did you do beforehand that likely led to this issue? Did you enable any of the hacks in Priiloader?
If you have access to the Homebrew Channel, follow this guide to post a sysCheck:
Also, do you have bootmii installed as boot2?
I was trying to install bootmii when I discovered the problem. The instructions on the website were really vague so I couldn't figure it out. The only things I installed were Nintendont which was working fine and priiloader. I activated the region free, and no update from disc/online system menu hacks but disabling them didn't fix anything.
System check below.
aa 01 bd 67, 7c 20 dc 28, 9c c6 b0 c9, 48 4b d3 f7, cd bc 4b 10
IOS57 base hash:
e7 46 07 56, 4c e8 69 2f, cd e1 19 02, 26 d6 a1 dd, 82 4c ef 0c
IOS56 base hash:
1b cc cf 07, f1 0c d5 12, be 96 9a a5, d2 36 67 98, 30 71 e6 81
IOS55 base hash:
c5 00 19 41, 22 18 21 92, b6 39 c9 d2, 05 fe 3f b3, 43 36 ae 0c
IOS53 base hash:
78 68 c0 50, 5c d6 d5 15, 65 d7 d8 0f, f0 a2 d9 d4, 9e 1d 7d fb
IOS48 base hash:
8d 53 7a 4a, 09 51 e5 6b, 2b 65 c8 27, f0 47 bb 72, c3 5c da e2
IOS46 base hash:
f5 e0 93 27, 26 cb 68 7b, ac e7 cc 86, 39 77 71 d1, ba 9e 42 36
IOS45 base hash:
08 58 11 20, 6b 3a e5 9f, b9 10 16 8b, 8a ea 06 3d, 9c 14 80 ef
IOS43 base hash:
f8 46 be 02, 74 e7 90 a3, d9 00 9a ae, d5 95 3f 77, e3 3f ad 2a
IOS41 base hash:
6c ad 7f 85, b6 87 e3 c3, 17 4e 5c 79, 99 fd 01 83, 16 55 fa 6f
IOS38 base hash:
f5 77 6b 66, cd 74 12 ee, 19 12 5c 11, 54 bf d7 3e, d7 e4 af 4b
IOS37 base hash:
32 c7 bc 54, 92 f6 17 e2, 64 26 e3 ce, bd 36 9f 40, 42 ea e8 02
IOS36 base hash:
29 36 80 06, 7d 22 7e 9f, 1c b1 af 70, 32 69 25 6d, 73 fb 14 55
IOS35 base hash:
58 5e 04 25, 45 d4 e2 8e, 98 fe 0d cd, 76 d0 71 d6, ac 17 a0 9c
IOS34 base hash:
68 8a 19 ae, c4 9f 57 fb, 11 1b 31 49, 2b 4d b4 85, 25 a6 3f 72
IOS33 base hash:
fc cf c4 1b, fc 8c 12 9e, 1f 67 5b 42, d4 3d 10 d6, 56 4f f5 f9
IOS31 base hash:
71 5f d8 87, 67 3e 32 4c, 53 c5 00 ce, 2b 50 14 f7, f2 ff e8 31
IOS28 base hash:
5c cd 08 24, 19 7b 9a 02, 17 55 5d f9, 39 dc dc 49, 73 ea 75 6a
IOS22 base hash:
8d 84 49 8b, f5 ba 6c a8, f0 58 64 10, 40 25 cd 1c, 25 9b 8a f6
IOS21 base hash:
91 ba e4 26, 1b 49 f0 95, e0 8c 21 17, e1 fa 8b e9, 92 6d eb 1b
IOS17 base hash:
77 7b 4c cb, 9a fb fe fc, 20 ee 4c 0e, 58 a1 6b ff, a0 20 a2 23
IOS15 base hash:
74 7c e3 33, 83 94 97 d7, a2 86 67 47, 55 61 83 0a, d0 3c 60 48
IOS14 base hash:
3d 56 0e 38, ce 93 90 4f, 42 b7 8f e9, b7 86 f1 a8, f9 39 b6 ce
IOS13 base hash:
5e a2 9d 72, 7e 56 37 26, 3f 62 3d 78, 1c 03 d2 f3, f5 40 52 5c
IOS12 base hash:
ba bf a4 78, da 4e 06 ec, f0 53 1a f0, 7f ad e2 eb, ff 3f cb 5d
IOS9 base hash:
7c 7a 60 0f, e4 85 77 89, 64 5a a1 a0, be a3 4d 59, 83 68 75 a6
IOS57 base hash:
e7 46 07 56, 4c e8 69 2f, cd e1 19 02, 26 d6 a1 dd, 82 4c ef 0c
IOS56 base hash:
1b cc cf 07, f1 0c d5 12, be 96 9a a5, d2 36 67 98, 30 71 e6 81
IOS55 base hash:
c5 00 19 41, 22 18 21 92, b6 39 c9 d2, 05 fe 3f b3, 43 36 ae 0c
IOS53 base hash:
78 68 c0 50, 5c d6 d5 15, 65 d7 d8 0f, f0 a2 d9 d4, 9e 1d 7d fb
IOS48 base hash:
8d 53 7a 4a, 09 51 e5 6b, 2b 65 c8 27, f0 47 bb 72, c3 5c da e2
IOS46 base hash:
f5 e0 93 27, 26 cb 68 7b, ac e7 cc 86, 39 77 71 d1, ba 9e 42 36
IOS45 base hash:
08 58 11 20, 6b 3a e5 9f, b9 10 16 8b, 8a ea 06 3d, 9c 14 80 ef
IOS43 base hash:
f8 46 be 02, 74 e7 90 a3, d9 00 9a ae, d5 95 3f 77, e3 3f ad 2a
IOS41 base hash:
6c ad 7f 85, b6 87 e3 c3, 17 4e 5c 79, 99 fd 01 83, 16 55 fa 6f
IOS38 base hash:
f5 77 6b 66, cd 74 12 ee, 19 12 5c 11, 54 bf d7 3e, d7 e4 af 4b
IOS37 base hash:
32 c7 bc 54, 92 f6 17 e2, 64 26 e3 ce, bd 36 9f 40, 42 ea e8 02
IOS36 base hash:
29 36 80 06, 7d 22 7e 9f, 1c b1 af 70, 32 69 25 6d, 73 fb 14 55
IOS35 base hash:
58 5e 04 25, 45 d4 e2 8e, 98 fe 0d cd, 76 d0 71 d6, ac 17 a0 9c
IOS34 base hash:
68 8a 19 ae, c4 9f 57 fb, 11 1b 31 49, 2b 4d b4 85, 25 a6 3f 72
IOS33 base hash:
fc cf c4 1b, fc 8c 12 9e, 1f 67 5b 42, d4 3d 10 d6, 56 4f f5 f9
IOS31 base hash:
71 5f d8 87, 67 3e 32 4c, 53 c5 00 ce, 2b 50 14 f7, f2 ff e8 31
IOS28 base hash:
5c cd 08 24, 19 7b 9a 02, 17 55 5d f9, 39 dc dc 49, 73 ea 75 6a
IOS22 base hash:
8d 84 49 8b, f5 ba 6c a8, f0 58 64 10, 40 25 cd 1c, 25 9b 8a f6
IOS21 base hash:
91 ba e4 26, 1b 49 f0 95, e0 8c 21 17, e1 fa 8b e9, 92 6d eb 1b
IOS17 base hash:
77 7b 4c cb, 9a fb fe fc, 20 ee 4c 0e, 58 a1 6b ff, a0 20 a2 23
IOS15 base hash:
74 7c e3 33, 83 94 97 d7, a2 86 67 47, 55 61 83 0a, d0 3c 60 48
IOS14 base hash:
3d 56 0e 38, ce 93 90 4f, 42 b7 8f e9, b7 86 f1 a8, f9 39 b6 ce
IOS13 base hash:
5e a2 9d 72, 7e 56 37 26, 3f 62 3d 78, 1c 03 d2 f3, f5 40 52 5c
IOS12 base hash:
ba bf a4 78, da 4e 06 ec, f0 53 1a f0, 7f ad e2 eb, ff 3f cb 5d
IOS9 base hash:
7c 7a 60 0f, e4 85 77 89, 64 5a a1 a0, be a3 4d 59, 83 68 75 a6