i just started have the EXACT same problem over the past week or so and came here looking for others with the same problem. i have had quite a few emails that are on my spamassassin whitelist end up in my junk mail folder. i have my entire webmail address book whitelisted, some of those are ending up in my junk folder. when they end up in the junk folder i select "move to inbox and whitelist sender", even though that email is already whitelisted, BUT the next time that person emails me it ends up right back into the junk folder.
this started happening in the last week or so. up until now i haven't had any issues with spamassassin and my whitelist.