pathauto_clean_string and accents from a bootstrap PHP file
After having a look at the code from the pathauto_cleanstring function, I would suggest testing the following:


Checking the value of pathauto_transliterate prior to calling the pathauto_cleanstring function 

variable_get('pathauto_transliterate', FALSE)     
If that value is FALSE, you probably found the reason. Try setting that variable to TRUE to force use of transliteration inside the pathauto_cleanstring function. N.B.: You only need to set this value once.

variable_set('pathauto_transliterate', TRUE), or
drush vset pathauto_transliterate TRUE    
Try your code again. Fingers crossed!


I suspect that your code never actually uses the transliterate function, but that is something that you can check by dumping the 'pathauto_transliterate' variable in the various scenarios where your code is executed (in-module, custom script, etc.)