I went back and checked the logs and these are the errors and info I got while the issue was happening, I edited out usernames and IP addresses for security:

20150513 11:06:36 [Scanner thread] INFO com.ubooquity.data.feeder.a - Scanning comics directories
20150513 11:06:36 [pool-2-thread-4] INFO com.ubooquity.b - Reverse proxy prefix is not activated
20150513 11:06:36 [Scanner thread] WARN com.ubooquity.data.database.b - Could not find id of root path J: (ignore this warning if you just added a new root directory)
20150513 11:06:36 [pool-2-thread-4] INFO com.ubooquity.b - Internal server started. Listening on port 2202
20150513 11:06:42 [Scanner thread] ERROR com.ubooquity.data.feeder.a - Error while scanning comics shared directories
java.lang.NullPointerException: null
at java.util.Objects.requireNonNull(Unknown Source) ~[na:1.8.0_45]
at java.util.Arrays$ArrayList.<init>(Unknown Source) ~[na:1.8.0_45]
at java.util.Arrays.asList(Unknown Source) ~[na:1.8.0_45]
at com.ubooquity.data.feeder.a.c(SourceFile:442) [Ubooquity.jar:1.7.6]
at com.ubooquity.data.feeder.a.b(SourceFile:39) [Ubooquity.jar:1.7.6]
at com.ubooquity.data.feeder.a$1.run(SourceFile:127) [Ubooquity.jar:1.7.6]
at java.lang.Thread.run(Unknown Source) [na:1.8.0_45]
20150513 11:06:42 [Scanner thread] WARN com.ubooquity.data.database.b - Could not find id of root path J: (ignore this warning if you just added a new root directory)
20150513 11:06:42 [Scanner thread] INFO com.ubooquity.data.feeder.a - Finished scanning comics directories, populating folders content cache
20150513 11:06:42 [Scanner thread] INFO com.ubooquity.data.feeder.a - Comics folder content cache populated
20150513 11:06:44 [pool-2-thread-14] INFO com.ubooquity.provider.webadmin.j - Admin logged off
20150513 11:06:55 [pool-2-thread-19] INFO com.ubooquity.b - User logged off
20150513 11:07:12 [pool-2-thread-19] INFO com.ubooquity.b - Cookie token invalid or too old. Access Denied. [login:][ip:216.47.218.231]
20150513 11:07:12 [pool-2-thread-19] INFO com.ubooquity.b - User successfuly logged in. [login:][ip:]
20150513 11:12:12 [pool-2-thread-11] INFO com.ubooquity.b - User logged off
20150513 14:36:08 [pool-2-thread-17] INFO com.ubooquity.b - User successfuly logged in. [login:][ip:]
20150513 14:37:21 [Scanner thread] INFO com.ubooquity.data.feeder.a - Scanning books directories
20150513 14:37:21 [Scanner thread] INFO com.ubooquity.data.feeder.a - Finished scanning books directories, populating folders content cache
20150513 14:37:21 [Scanner thread] INFO com.ubooquity.data.feeder.a - Books folder content cache populated
20150513 14:37:21 [Scanner thread] INFO com.ubooquity.data.feeder.a - Scanning comics directories
20150513 14:37:21 [Scanner thread] WARN com.ubooquity.data.database.b - Could not find id of root path J: (ignore this warning if you just added a new root directory)
20150513 14:37:24 [Scanner thread] INFO com.ubooquity.b.c - Reading metadata of comic file: J:\\Comics\Misc\Mad Max - Fury Road Inspired Artists Deluxe Edition (2015) (Digital) (Dogmatix-Empire).cbr
20150513 14:37:24 [Scanner thread] INFO com.ubooquity.data.database.b - Inserting/updating comic entry in database : J:\Comics\Misc\Mad Max - Fury Road Inspired Artists Deluxe Edition (2015) (Digital) (Dogmatix-Empire).cbr
20150513 14:37:31 [Scanner thread] ERROR com.ubooquity.data.feeder.a - Error while scanning comics shared directories
java.lang.NullPointerException: null
at java.util.Objects.requireNonNull(Unknown Source) ~[na:1.8.0_45]
at java.util.Arrays$ArrayList.<init>(Unknown Source) ~[na:1.8.0_45]
at java.util.Arrays.asList(Unknown Source) ~[na:1.8.0_45]
at com.ubooquity.data.feeder.a.c(SourceFile:442) [Ubooquity.jar:1.7.6]
at com.ubooquity.data.feeder.a.b(SourceFile:39) [Ubooquity.jar:1.7.6]
at com.ubooquity.data.feeder.a$1.run(SourceFile:127) [Ubooquity.jar:1.7.6]
at java.lang.Thread.run(Unknown Source) [na:1.8.0_45]
20150513 14:37:31 [Scanner thread] WARN com.ubooquity.data.database.b - Could not find id of root path J: (ignore this warning if you just added a new root directory)
20150513 14:37:31 [Scanner thread] INFO com.ubooquity.data.feeder.a - Finished scanning comics directories, populating folders content cache
20150513 14:37:31 [Scanner thread] INFO com.ubooquity.data.feeder.a - Comics folder content cache populated

I can send u the full log if u like?

I had the black screen issue pop up right after adding a new user and allowing him access to comics via the web admin page. Like the OP, I had the links but nothing showed up. I even added a new book to see if it would show up, it didnt. I fixed mine by removing the share path to my comics and re-adding it in Ubooquity. Not sure if this helps you track down anything but: I have my comics stored on a separate pc from the Ubooquity server. I have a mapped drive setup on the Ubooquity Server and used that path in the Ubooquity settings.