On server-side, in your VB.NET code, you should be able to find your control by the ID you gave it. So, if you had something like
You can access it on your server-side by calling FindControl("myPlaceHolder"). What you're seeing, "ctl00_CPHPContent_" is .NET's way of making sure each element on the front end (read: HTML) all have unique IDs across the board, so it gives it names denoting its location on the page, etc.
So, if I understand you correctly, you're using FindControl("ctl100_CPHPContent_myPlaceHolder") and it's coming up null? Or are you using FindControl("myPlaceHolder") and it's not finding the control?
Another thing to keep in mind is how you're getting the control on the page? Are you writing it into the aspx or ascx file, or are you created it dynamically in VB.NET? If it's the later, be sure you're creating dynamic controls during the correct stage of the page lifecycle, i.e. in Page_Init.
Hope that helps a little.