Your comments

This.

There is already page preloading, but it's not working in all situations and deserves improvement.
It's planned as part of the enhanced online comic reader.
Seems to be a H2 database bug.
I'll migrate to the latest version of H2 for the next Ubooquity release, that should make this bug disappear.

In the meantime, you can work around this problem by running Ubooquity in any non-root folder (i.e. create a folder on E: and run Ubooquity in it instead of running it directly at the root of your disk).

Took me some time but I added Chnuky Reader as my recommended reader for iPad in the FAQ.
All the files and folders Ubooquity creates (including the cached thumbnails and the database) are located in the "working directory".
The working directory is simply the directory where you are when you launch Ubooquity.
So, for instance, if Ubooquity.jar is in /apps but you want it to create its files in /another/folder/, simply go ("cd" command) in /another/folder/ and run Ubooquity by giving its full path to the java command.
Something like:

java -jar /apps/Ubooquity.jar
If you use a Windows shortcut, the working directory is a field you can define in the properties of your shortcut.

Last way of specifying the working dir: pass the user.dir parameter to java when running Ubooquity.

java -Duser.dir=<your folder> -jar Ubooquity.jar
Replace "<your folder>" by the absolute path of the location where you want Ubooquity files to be written.

Let me know if you have any question.