For a possible explanation you'll have to consider the following:
The TARDIS translates (almost) everything so it can be perceived and understood by those travelling with it. This includes spoken and written words.
After this scene the Doctor notes that it's been a message and coordinates, so he travels to ancient Britain:
Just followed the co-ordinates on the cliff face. Earth. Britain. one oh two am. No, pm. No, AD.
Considering there's no other writing on the cliff (at least nothing seen by Amy and the audience), this has to be the information in the second line. However to me this creates a few new questions that can't necessarily be explained by what we see in the episode:
- The characters appear to be of Greek origin, which doesn't make any sense (why weren't they translated as well? Or why were they translated into Greek?).
- There are only 7 characters in 3 groups, making it impossible to include/encode all the information that's supposed to be in there. Remember that River knew exactly the point in time and space where the Doctor would arrive (sending the Roman soldier to welcome Caesar). So it's more precise than just "Britain 102 AD", but where is that information coming from?
What I think
It's possible to interpret the second line as Greek numerals:
ΘΣ: 9 200
ΓΥΔϟ: 3 400 4 90
This doesn't sound that far off thinking about it - in fact it's my favorite theory right now. The information "on Earth" doesn't necessarily have to be included - neither does "to the Doctor", considering it's more or less River's home planet and it's clearly written by River. So with more specific details missing, it should be obvious she's talking about Earth.
The first two groups (ΘΣ Φ) could represent a coordinate pair to identify a specific point on the surface of the Earth and the last group (ΓΥΔϟ) would mark a specific point in time. Once again, there'd be an offset given by the fact the message is from River.
Since I completely missed the clickable link regarding the Theta-Sigma reference, I skipped that. So here's an alternative interpretation with one more tiny assumption:
- The first two Greek characters (ΘΣ) refer the Doctor as the intended recipient.
- This leaves five more numerals for space and time (at least 3 dimensions).
Since there are only two groups, you'll have to add one more space that's omitted for whatever reason (might be a goof):
- Φ: 500
- ΓΥ: 3 400
- Δϟ: 4 90
This doesn't sound that far off, because now the grouping makes more sense (the second and third coordinate being grouped, having a small number as well as a big one).
The question left is just how you could use those to get usable coordinates (longitude, latitude, and time).
This is pure speculation, but it makes sense in some way:
- Let's just assume the Doctor's coordinates would work like humankind's longitude/latitude system, so Greenwich would denote 0°.
- Since Stonehenge isn't that far away, I could accept the first number being the longitude, while the second number being the latitude.
- Finally, the last number would denote the time, although this would still be rather rough given the fact that the Doctor seems to arrive just in time and not just within a general time frame (or it's just a rough estimate and the TARDIS would be able to determine the rest)? This would support the Doctor's confusion regarding am/pm/AD.
- Since the Greek numerals don't make any direct sense the way they're used (they wer used in a decimal system), I could imagine this being based on a different scaling.
- If you assume for time, the second digit to the right denotes 3 years rather than 10 years, you'd end up with 3 * 4 + 90 = 102... Eureka! Okay, it's really just speculation and trying to find a formula, which isn't that hard with only two numbers.
Although this still doesn't explain why the numbers don't show up using arabic numbers or anything more easily perceivable. Maybe the TARDIS isn't able to get the proper meaning (i.e. it doesn't know whether this is supposed to be words or numbers) or it's part of River's plan to hide the message right in the face of the whole universe to only be seen (and understood) by the Doctor.