I have noticed the following:
var b1 = Regex.IsMatch(\"Line1\\nLine2\", \"Line1$\", RegexOptions.Multiline); // true
var b2 = Regex.IsMatch(\"Line1\\r\\nLi
From MSDN:
By default, $ matches only the end of the input string. If you specify the RegexOptions.Multiline option, it matches either the newline character (\n) or the end of the input string. It does not, however, match the carriage return/line feed character combination. To successfully match them, use the subexpression \r?$ instead of just $.
http://msdn.microsoft.com/en-us/library/yd1hzczs.aspx#Multiline
So I can't say why (compatibility with regular expressions from other languages?), but at the very least it's intended.