Welcome emails in particular, are frequently considered spam (e.g. http://www.elkarte.net/community/index.php?topic=4052.msg29000#msg29000 ).
It may be worth tweaking a bit the text to reduce the perception of spam?
Maybe reduce the URLs/text ratio?
I'm not sure if it may make any difference, but looking at the various welcome email I received in the past, it looks like they have some more text and less different URLs.
For example, I just registered at xenforo and the email contains 2 URLs:
1) the forum URL,
2) the activation URL.
To say the truth, the URLs are spread across 5 links.
Another thing I noticed is the plain-text version of the email contains only the activation URL.
For sure we can cut down on the number of links, that should help. I don't think the "backup" system links of the code are needed in the first email, maybe only in the reminder email, or whatever. A bit more wordiness would help as well, lets compare to what some of the other software does for this.