Logitech Media Server 7.81 and 7.90 Not Finding All Files

This is driving me nuts! I just finished setting up a new Drobo 5d which contains all of my music files in flac. Instead of many different hard drives that I have to point to, now I just have one. I am running Windows 7 64bit on a PC. My music files are located in D:\My Music and my playlists are in D:\My Music\My Playlists. No matter which version of LMS (the last one I tried was 7.90) I install, the same thing happens - it scans for a few minutes, than says it is finished rescanning, but it says "6633 albums, 0 artists" and there are no playlists. I have over 6tb of music files, so there should be a heck of a lot more than that. I am probably doing something wrong that one of you experts can point out to me.

Here is my last scan log:

[15-03-05 10:18:14.7093] Slim::Utils::SQLHelper::executeSQLFile (85) Error: Couldn't execute SQL statement: [DELETE FROM comments;] : [Carp::Clan::__ANON__(): DBI Exception: DBD::SQLite::db do failed: database disk image is malformed [for Statement "DELETE FROM comments;"] at /<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Schema/Storage.pm line 126
]
[15-03-05 10:18:14.7142] Slim::Music::Import::runImporter (485) Starting Slim::Media::MediaFolderScan scan
[15-03-05 10:18:14.7145] Slim::Utils::Scanner::Local::rescan (177) Discovering audio files in D:\My Music
[15-03-05 10:21:42.8780] Slim::Utils::Scanner::Local::__ANON__ (188) Start processing found tracks
[15-03-05 10:21:42.8783] Slim::Utils::Scanner::Local::__ANON__ (196) Connect do DB
[15-03-05 10:21:42.8785] Slim::Utils::Scanner::Local::__ANON__ (199) Get latest ID
[15-03-05 10:21:42.8788] Slim::Utils::Scanner::Local::__ANON__ (221) Delete temporary table if exists
[15-03-05 10:21:42.8791] Slim::Utils::Scanner::Local::__ANON__ (224) Re-build temporary table
[15-03-05 10:21:42.9621] Slim::Schema::Storage::throw_exception (122) Error: DBI Exception: DBD::SQLite::db do failed: database disk image is malformed [for Statement "
CREATE TEMPORARY TABLE diskonly AS
SELECT DISTINCT(url) as url
FROM scanned_files
WHERE url NOT IN (
SELECT url FROM tracks
WHERE id <= 77502
)
AND url LIKE 'file:///D:/My%20Music%'
AND filesize != 0
"]
[15-03-05 10:21:42.9628] Slim::Schema::Storage::throw_exception (122) Backtrace:

frame 0: Slim::Utils::Log::logBacktrace (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Schema/Storage.pm line 122)
frame 1: Slim::Schema::Storage::throw_exception (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>DBIx/Class/Storage/DBI.pm line 1006)
frame 2: DBIx::Class::Storage::DBI::__ANON__ (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Utils/Scanner/Local.pm line 225)
frame 3: Slim::Utils::Scanner::Local::__ANON__ (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Utils/Scanner/Local/Async.pm line 84)
frame 4: Slim::Utils::Scanner::Local::Async::__ANON__ (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Utils/Scanner/Local/Async.pm line 167)
frame 5: Slim::Utils::Scanner::Local::Async::find (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Utils/Scanner/Local.pm line 102)
frame 6: Slim::Utils::Scanner::Local::find (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Utils/Scanner/Local.pm line 544)
frame 7: Slim::Utils::Scanner::Local::rescan (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Media/MediaFolderScan.pm line 67)
frame 8: Slim::Media::MediaFolderScan::startScan (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Music/Import.pm line 487)
frame 9: Slim::Music::Import::runImporter (/<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Music/Import.pm line 333)
frame 10: Slim::Music::Import::runScan (scanner.pl line 332)
frame 11: (eval) (scanner.pl line 326)
frame 12: main::main (scanner.pl line 504)

[15-03-05 10:21:42.9635] main::main (337) Error: Failed when running main scan: [Carp::Clan::__ANON__(): DBI Exception: DBD::SQLite::db do failed: database disk image is malformed [for Statement "
CREATE TEMPORARY TABLE diskonly AS
SELECT DISTINCT(url) as url
FROM scanned_files
WHERE url NOT IN (
SELECT url FROM tracks
WHERE id <= 77502
)
AND url LIKE 'file:///D:/My%20Music%'
AND filesize != 0
"] at /<C:\PROGRA~2\SQUEEZ~1\server\scanner.exe>Slim/Schema/Storage.pm line 126
]
[15-03-05 10:21:42.9639] main::main (338) Error: Skipping post-process & Not updating lastRescanTime