ohhh i see ... custom isn't global optiion - it's local ... need to be set als parameter whdload game.slave preload; custom1=1 (untested! next few days)
your whdlGenerator.py: fStartupSeq.write("WHDload "+slaveFile+" Preload\n")
... that makes it even more complicated: ( I can't even think of an easy workaround - just quick&dirty ... 
So you just made me lose my time by spilling nonsense about a file which isn't concerned at all....
Nonsens? It's your file ... you start whdload with this line. Custom1 is an local-parameter which start like whdload game.slave preload custom1=1 (theoretical; i don't test this at the moment): https://fs-uae.net/whdload-support/comment-page-4 - there is an example ...
But: if you offer whdload-Support - please read yourself in ... i am only a user and it is not my job to find solutions - it is your job if you want integrated Amiga-Support official in Recalbox!
The problem with this call: it applies to everyone. So one would have to define in advance for whom this applies. Quick&Dirty: Optional extra file (per game) which contains only the local call - add the content to it. Quick&Dirty = no practical solution! Did you have an idea?
I asked Horace @ Facebook for a solution (sorry for that .. but I want a solution for my problem!). It even exists - is called whdload booter. But it's designed for retropie - but he said it runs without any retropie. http://www.ultimateamiga.co.uk/HostedProjects/RetroPieAmiga/downloads/ --- a. ws file with extra parameters is required for each game. I will checks this the next few days ...
Refresh is a good friend.
But this problem was with your old install (sometimes it happends that an .adf copied into whdload-dir...). At the moment for this point no problem. The "question" was whether you are doing something different here than in the old version. If not, it is still vulnerable to error. But very hard to find it out
[With the old installation the 5-6x happened ... in 2-3h testing!]
If was not the case either with old install, this bug was corrected a long time ago
More nonsense.
definitly not corrected in OLD Install! Sorry! I've used the latest version (from your old install) - it happends very often on my tests on Sunday. But if you corrected this in install - everything is ok - done! I don't know which bugs you have fixed vom old to new Install ... it was more than just info in case it wasn't known and so it was taken over 1:1. Sorry.....
Next example? Standard-CPU for Amiga600 is 68000 (amiberry!) ... Historyline, Settler needs minimum 68020. User xyz know " its amiga 500 - i put it into amiga600" - and don't work - cpu to low. OK it is possible to change cpu in .uae. But ... all this things ... here cpu x, there more chipmen, many whdload-games are to fast
Then use this games on Amiga1200 and they will work fine without config !!! This works for 95% of the WHDL games
User doesn't then need to do anything and if they do they just need to modify the uae manually.
I just want to help here! Sorry for that!
I know how to get this stuff running. But Recalbox is a Copy&Run/Easy-to-Use installation. When the users see: Amiga 500 game - they will put it in the 600 folder... and then ask HERE why it doesn't work. I'm just giving you a preview of what's coming!
OK, this last exchanges definitely prove to me that :
- you're not willing to explain correctly what you want or do
- you have a attention span of approximatively 2s
- you're not listening to what others are saying
- you spill nonsense more than usual, especially when you're unsure about something or when you don't even know what you are doing
So I definitely do not have time for that, please be on your own from now on and don't bother me anymore
Sorry for help ... sorry for testing your installation (and spend many time into it) ... sorry for find an solution for whdload problems
I didn't explain correctly? Did you have check the Wings-Problem? TEST IT! It doesn't save. I've explain exactly the way what i do and described the conditions under which a savegame is stored (exit/save in GAME-Main-Menu -> and then kill uae4arm; Disk-Version: Autosave progress).
Listing to other? We are the only one to talk about this. You hope that every people use only one of the 95% games who works. I have only 20-30 whdloadgames ... Historyline don't work without local whdload-parameter (very popular game in german), SlamTilt not saving, Wings problems with autosave (3 Games with problems from 30, but only max 10 tested! definetly more than 5%!). Solution should be an global parameter - look @ horace whdload booter.zip -> S/whdload.prefs ... NoWriteCache is activated. NoWriteCache means: everything is writing DIRECTLY to disk and not after leave the game over ingame exit/save-Option:
https://circuit-board.de/forum/index.php/Thread/18365-A500-mit-WHDLoad-Cannon-Fodder-Savegame-ist-nach-Neustart-weg-Problem-gelöst/ (sorry german)
http://eab.abime.net/showthread.php?t=64818
http://www.minimig.net/viewtopic.php?f=3&t=356 <- ok it should be a problem with 68000 CPU (your Amiga600-Config) ... NoWriteCache need with this CPU. Ok your solution: use Amiga 1200....... right?
I am a 5%-Gamer - Sorry 
You're not listing to what others are saying! Sorry!
New Bug?
Multidisk Amiga600
Wings Disk 1.adf
Wings Disk 2.adf
I've started Wings Disk 1.adf
Don't work - i must go to the UAE-Menu: Floppy -> First Floppy has inserted Disk 2! Second Floppy = Disk 1; I must swap Floppy 0 / 1 -> Reset. Work.
Sorry for find this ... and waste your time ... 95%-Gamer don't Play Multidisk-Games..... 
Disk 1 of 2.adf better? I don't see in adfGenerator.py that you are look after "Disk 1". You count by yourself the disks? Right? so there's no difference between "disk 1.adf" and "disk 1 of 2.adf". Sorry for waste your time again. It should be an 5%-Gamer-Problem 