FYI, I can't replicate the problem. I always get 6 days apart, even with 11/1/2008 (and even when pretending to be in another time zone, e.g. via TZ=PST).  Not really sure if it might have to do with the timezone, but maybe you could just try by switching to timegm()/gmtime() (and $ENV{TZ}="GMT", as strftime is TZ-aware).  Or maybe your system's POSIX library (strftime) is just broken...

Update: actually, I can reproduce the issue when using a time zone for which my system does handle daylight savings time¹ (plus using a different start date, as in (most parts of) Europe the DST switch is done on the last Sunday in October — as opposed to the first Sunday in November).  Similarly, using TZ=GMT 'fixes' the issue:

$ TZ=CET ./727202.pl -s 10/25/2008
The start day is 10/25/2008 and the end day is 10/30/2008 23:00
$ TZ=GMT ./727202.pl -s 10/25/2008
The start day is 10/25/2008 and the end day is 10/31/2008 00:00
[download]

(to show the hour, I changed the end_day format to "%m/%d/%Y %H:%M")

Anyhow, as others have said, it's probably better to use a module that has already solved this, and other date/time issues...

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¹ For reasons I haven't investigated further, it isn't sufficient to set my TZ to a time zone in the US — when doing so, I do get the respective local time, but without the local daylight savings time being handled correctly... (which is why I initially couldn't replicate the problem)