That sounds like the Color Picker, which works a bit differently in ID than in Illustrator or Photoshop. If the cursor is not in one of the RGB fields when you say OK you won't get RGB color. You can see this by noting the text in the Add ... Swatch button. My guess is you added the color as the CMYK conversion which is a bit lighter.
You might want to use the panel menu in the Swatches panel instead, or the new swatch button at the bottom of the panel while holding down the Alt key to open the new swatch definition dialog. You want to create a Process color and change the type to RGB, then enter the values in the RGB fields. Or if what you want is really Pantone 249U you can define a Spot swatch and choose Pantone Solid Uncoated and then specify the 249. I'll warn you though, that CS6 uses Lab values for displaying spot colors and 249U is considerably lighter than either the RGB you specified or the 249C. In earlier versions the book value conversions were used. Even when using Lab display values through Ink Manager in CS5, the coated and uncoated swatches incorrectly look the same in ID, and in Illustrator CS5 you would need to turn on overprint preview to see a difference.
Here are a couple of screen captures from PDFs exported from ID CS5 and CS6 using High Quality Print. The colored boxes with the lables were pasted from Illustrator CS5 to be sure I was using the same color definitions and that theywere behaving as native objects. Below are the same boxes placed:
and here is how the screen looked in CS6 in ID (notice the difference in the placed .ai file -- the screen preview is NOT using the Lab values, although it exports with them):
I don't know what the content is and how you present it, but it doesn't sound like a web page. That said, if you choose Web for intent in Document Setup you can still use print size paper sizes for the document and change the rulers after the doc is created to read inches or millimeters or other units of your choice instead of pixels and the file will use default RGB swatches and default to RGB when making new colors.