most of the "problems" you've encountered are probably caused by the fact the script does not execute normaly with your server setup.
1. X_ name prefix is added when the exact image path/name already exists, the script is designed to check the db for an existing file not the ondisc file which could very well be missing in the db.
The fact it had to create "new" files with the same original name obviously follows a problem when executing the script. File was probably being added and the script failed for a reason. Reloading the script would try to add the very same file thus producing a 1_, then 2_ new files if several failures occur.. and that you want to force it by reloading..
2. The automated execution is not perfect, it's basically designed to try avoiding script timeouts but that doesn't work 100% and i even saw on some setups that it won't work at all.. i'd suggest you lower the number of pictures added in one pass, it won't matter if you add 5 pics or 10 at a time.. the only thing you want here is to avoid script failures..
3. look for "0750" values in the script and change them to whatever you want, "0755" in your case maybe.. i've also seen some setups that will not let mkdir change the default chmod value so it may not work..
4. failure to add pictures are probably cpg functions related, the script only makes sure the pics are not already in the database and then tries to add the new pictures using available cpg functions.. Once again it could fail if your remote picture takes too long to be fetched but then that's another timeout problem you'll have to deal with..
5. no idea where that come from, make sure you didn't see them in a gallery being updated. the relative index that cpg produces to access pictures in ablums is really relative and a single link would point to different pictures at different times if the gallery you browse is being updated..
6. Funny, i had the very same bug but only after i introcuded it myself while making modifications to my script..
So in your case it could also be related to your various script failures and so on..
My opinion is that it's absolutely not related in any ways to your cpg version, i've added like 5k pics to my demo gallery upgraded to 1.48 and had no problems whatsoever..
failure to add pictures can occur for various reasons since you rely on ip transfers which are themselves not reliable..