Version 1.10.0 did not solve the problem in your case ?

My bad, I'll fix that too in 1.10.1 (which will be done as soon as I have an hour to do it).

You're welcome. :)
I'll release shortly a new version (1.10.1) that automatically sets this flag.

I don't know why your version of Java did not include the new color management library used by Java 8 (Little CMS, the missing "javalcms" you had in your log), but if you have this problem, others might have it too.
I'll force Ubooquity to use the old library instead (hence the flag).

Could you try launching Ubooquity with the following command line parameter ?

-Dsun.java2d.cmm=sun.java2d.cmm.kcms.KcmsServiceProvider

Place it after "java", something like:

java -Dsun.java2d.cmm=sun.java2d.cmm.kcms.KcmsServiceProvider -jar ...

Which Java version are you using : Oracle or OpenJDK ?

Symbolic links problem fixed. See release notes.

PDF problem fixed, see release notes.

It's already near the top of my todo list. :)

I would be tempted to say that this is a CSS issue and that Ubooquity does not support IE (too complex and too different from other major browsers), but since it was working a few weeks ago, I don't know what to say. :(

You already tried the usual investigation steps...