I think I know what the problem is (was).

When running modrana from command line, it says:

cannot create directory, file already exists: '/home /user/.modrana'

however, as I said, I had not seen that directory. So I get into my phone via ssh and I see that it does exist /home/user/.modrana, but I was not able to cd into it because it is owned by the root user:

-rw-r--rw- 1 root root 4740 Jul 25 11:46 .modrana

I tried to get inside that directory, but I do not know why I could not. I thought it was a matter of permissions, but it was not:

Nokia-N900-51-1:/home/user# chmod 777 .modrana
Nokia-N900-51-1:/home/user# cd .modrana
-sh: cd: can't cd to .modrana

I erased it, and after that, I ran modrana again, and now I have the proper .modrana directory:

Nokia-N900-51-1:/home/user# ls -l .modrana
-rw-r--r-- 1 user users 3108 Aug 2 11:08 map_config.conf
-rw-r--r-- 1 user users 2024 Aug 2 12:39 options.bin
-rw-r--r-- 1 user users 5196 Aug 2 11:08 user_config.conf

Curious thing is, I do not remember that I have created that .modrana directory as root.

Here, pastebin before the "workaround", and here, the pastebin after.