Only scans a few hundred comics (over 5k in library), then stops ("Could not open file" )

I've been trying to get Ubooquity working in docker via popular docker image (https://github.com/hurricanehrndz/ubooquity) and also via a fork of that with some fixes I've found from here: http://ubooquity.userecho.com/topics/84-comics-not-imported-umlaut-mark-bug/

No matter what I do though, Ubooquity only scans ~315 comics. First, everything looks fine, a few hundred lines like this:

20160429 23:41:31 [Scanner thread] INFO com.ubooquity.data.database.b - Inserting/updating comic entry in database : /media/comics/Adventure Time
20160429 23:41:31 [Scanner thread] INFO com.ubooquity.b.c - Reading metadata of comic file: /media/comics/Adventure Time/Adventure Time 001.cbr

However there are also a few like this, getting permission denied errors:

20160429 23:40:56 [Scanner thread] WARN com.ubooquity.f.a - Failed to read file, will try to guess format: /media/comics/Dark Horse Presents/Dark Horse Presents 140.cbr20160429 23:40:56 [Scanner thread] WARN com.ubooquity.f.a - Could not read header of archive: /media/comics/Dark Horse Presents/Dark Horse Presents 140.cbr20160429 23:40:56 [Scanner thread] WARN com.ubooquity.f.a - Failed to guess file format20160429 23:40:56 [Scanner thread] INFO com.ubooquity.data.database.b - Inserting/updating comic entry in database : /media/comics/Dark Horse Presents/Dark Horse Presents 140.cbr20160429 23:40:56 [Scanner thread] WARN com.ubooquity.f.a - Could not open file: /media/comics/Dark Horse Presents/Dark Horse Presents 140.cbrjava.io.FileNotFoundException: /media/comics/Dark Horse Presents/Dark Horse Presents 140.cbr (Permission denied)      at java.io.RandomAccessFile.open(Native Method) ~[na:1.7.0_95]      at java.io.RandomAccessFile.(RandomAccessFile.java:241) ~[na:1.7.0_95]
      at com.github.junrar.io.ReadOnlyAccessFile.(ReadOnlyAccessFile.java:39) ~[junrar-0.7.jar.5968508007590811661.tmp:na]
      at com.github.junrar.impl.FileVolume.getReadOnlyAccess(FileVolume.java:46) ~[junrar-0.7.jar.5968508007590811661.tmp:na]
      at com.github.junrar.Archive.setVolume(Archive.java:581) ~[junrar-0.7.jar.5968508007590811661.tmp:na]
      at com.github.junrar.Archive.(Archive.java:108) ~[junrar-0.7.jar.5968508007590811661.tmp:na]
      at com.github.junrar.Archive.(Archive.java:113) ~[junrar-0.7.jar.5968508007590811661.tmp:na]
      at com.ubooquity.fileformat.cbr.a.a(SourceFile:40) ~[Ubooquity.jar:1.9.1]
      at com.ubooquity.f.a.a(SourceFile:89) [Ubooquity.jar:1.9.1]
      at com.ubooquity.f.a.a(SourceFile:43) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.b.a(SourceFile:67) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.a.b(SourceFile:531) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.a.c(SourceFile:470) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.a.b(SourceFile:35) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.a$1.run(SourceFile:123) [Ubooquity.jar:1.9.1]
      at java.lang.Thread.run(Thread.java:745) [na:1.7.0_95]

Then after a while it can't read directories at all?

20160429 23:31:09 [Scanner thread] INFO com.ubooquity.data.database.b - Inserting/updating comic entry in database : /media/comics/Some Comic Name
20160429 23:31:09 [Scanner thread] ERROR com.ubooquity.data.feeder.a - Error while scanning comics shared directories
java.lang.NullPointerException: null
      at java.util.Arrays$ArrayList.(Arrays.java:2842) ~[na:1.7.0_95]
      at java.util.Arrays.asList(Arrays.java:2828) ~[na:1.7.0_95]
      at com.ubooquity.data.feeder.a.c(SourceFile:454) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.a.b(SourceFile:35) [Ubooquity.jar:1.9.1]
      at com.ubooquity.data.feeder.a$1.run(SourceFile:123) [Ubooquity.jar:1.9.1]
      at java.lang.Thread.run(Thread.java:745) [na:1.7.0_95]

I have plenty of memory available, and the files/folders are all set to 777 permissions.

Max memory: 1324 MB
Free memory: 168 MB
Total memory: 415 MB

The library is ~5500 comics , in ~600 folders. But it seems like it's able to add the first ~300 comics just fine, no warnings or errors--then looks like it can't open any other directories

I also have a non-docker version of Ubooquity (same version) that works fine, running on the same exact device. No idea where to start, or what the actual problem might be.