Only a part of hard disk partition gets indexed

[HighCast]

Hi,

I upgraded my Subsonic server's hardware to a bit modern and also the operating system got updated.
The hard drive changed from multiple 2.5-inch HDD disks to one 3,5-inch 3TB hard drive.

The hard disk is partitioned to a 2x1TB + 760 Gb partitions. All are in exFAT type.

First I imported (through network share) files from one 320 gb 2.5-inch drive. There was about 110 Gb or MP3 files that were stored as standard setup on NTFS file system.
Then I indexed it - all went fine.

Then I imported 290 Gb from another old hard drive - again through network share. These files at the original drive were in "compressed" mode on NTFS system (so the file used Windows features to compress the content). The move went well, but after I tried to index the one and only Subsonic partition where the files all are, the amount of indexed data did not change. Nor did the count of files. Log does not reveal anything special through the link ribbon - I've not checked the log file itself.

What could cause such issues?
The Subsonic server is built as follows:

Intel i5 4-core cpu, 2,67 GHz
12 Gb RAM
Windows 8.1 x64
Subsonic 4.9 (build 3853)
jetty-6.1.x, java 1.7.0_51, Windows 8 (79,3 MB / 145,0 MB)

The server machine hosts also Plex server for video files, but those are hosted on another partition so this should not affect to this, as Plex does not interfere Subsonic.

Help would be greatly appreciated.