I do agree that your logo's color don't fit the site. Actually, it's shape doesn't really agree either. Anyway, your site looks really good otherwise.
The only thing I would suggest you change is in your Portfolio page. The websites for PureBox and Shells365 feature the same black server boxes in their header. You should not show any hint that you may reuse/rehash previous work. A customer is self-centered and is only interested in a unique product custom made for them.
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PureBox.net and Shells365.com, both are our company's website, of which we've closed the "shells365", however the first page is still there to show out the piece of work over that website, and about the "server" it is termed as 'symetry' to be displayed on our own websites, and i guess using a same gfx for our network websites, should not be considered as "reuse/rehash/recycle" =) thanks for the comments though,
for IDS the logo, we're using it for the past 5 years, the color scheme of logo is our identity now, however yes the necessary changes would be made to the logo to make it looks with accordance to the page. thank you for your kind comments. =)