Hello,
the problems you're describing are bugs, already known. Hopefully I
will get out the 1.5.4 update soon, which will be released for Linux,
too.
For the Grenouille quest, you may open the file quests.txt with an
editor and search for his name. Then, you should fine a line where all
needed ingredients are listed (separated by , ). Change "bottle of
water"
to "water" and the quest should work once you start again.
Regarding Dr. Zimmermann, there's unfortunately nothing you can do at
the moment, but wait for 1.5.4. Sorry ...