I run "pwb.py login -all", and everything seems ok:
pwb.py login -all
Password for user MalafayaBot on wiktionary:el (no characters will be shown)
Logging in to wiktionary:el as MalafayaBot
Logged in on wiktionary:el as MalafayaBot.
Logged in on wiktionary:en as MalafayaBot.
Logged in on wiktionary:zh as MalafayaBot.
Logged in on wiktionary:ca as MalafayaBot.
Logged in on wiktionary:vo as MalafayaBot.
Logged in on wiktionary:io as MalafayaBot.
Logged in on wiktionary:ia as MalafayaBot.
Logged in on wiktionary:gl as MalafayaBot.
Logged in on wiktionary:es as MalafayaBot.
Logged in on wiktionary:az as MalafayaBot.
Logged in on wiktionary:nl as MalafayaBot.
Logged in on wiktionary:nn as MalafayaBot.
Logged in on wiktionary:no as MalafayaBot.
Logged in on wiktionary:tr as MalafayaBot.
Logged in on wiktionary:li as MalafayaBot.
Logged in on wiktionary:lt as MalafayaBot.
Logged in on wiktionary:vec as MalafayaBot.
Logged in on wiktionary:ro as MalafayaBot.
Logged in on wiktionary:is as MalafayaBot.
Logged in on wiktionary:fr as MalafayaBot.
Logged in on wiktionary:bg as MalafayaBot.
Logged in on wiktionary:uk as MalafayaBot.
Logged in on wiktionary:de as MalafayaBot.
Logged in on wiktionary:mg as MalafayaBot.
Logged in on wiktionary:da as MalafayaBot.
Logged in on wiktionary:br as MalafayaBot.
Logged in on wiktionary:bs as MalafayaBot.
Logged in on wiktionary:fi as MalafayaBot.
Logged in on wiktionary:hu as MalafayaBot.
Logged in on wiktionary:ka as MalafayaBot.
Logged in on wiktionary:pt as MalafayaBot.
Logged in on wiktionary:oc as MalafayaBot.
Logged in on wiktionary:sv as MalafayaBot.
Logged in on wiktionary:ku as MalafayaBot.
Logged in on wiktionary:nds as MalafayaBot.
First odd thing: file pywikibot.lwp has been changed but it's contents is simply one line:
#LWP-Cookies-2.0
I then run interwiki for example:
pwb.py interwiki pt:Categoria:Arquitetura
Password for user MalafayaBot on wiktionary:pt (no characters will be shown):
Logging in to wiktionary:pt as MalafayaBot
Retrieving 1 pages from wiktionary:pt.
[[pt:Categoria:Arquitetura]]: [[pt:Categoria:Arquitetura]] gives new interwiki [
[ast:Categoría:Arquitectura]]
[[pt:Categoria:Arquitetura]]: [[pt:Categoria:Arquitetura]] gives new interwiki [
[az:Kateqoriya:Memarlıq]]
[......]
Again, it asked for credentials. For each new run, I have to enter credentials.
If you intend to reproduce this issue, it's probably best to delete your pywikibot.lwp file first.