This would mean switching gears for you, but I'll throw my suggestion out there anyhow.

Instead of hanging curtains that will be awkwardly short (curtains often look odd when they're not floor length), why not hang roman shades? Bamboo or fabric roman shades would cover your windows without having to be hemmed or hang awkwardly short of the floor in order not to be a fire hazard.

I would suggest hanging both shades at the same height (This will mean that the shade is hanging several inches above the shorter window). This will make both windows appear to be the same height.

Here is a link that might be useful: Google image search for roman shades to show examples

Yes, I agree with bsmith. Then, if you want to keep the drapes, raise the rod on the one window and keep the curtains stationary. They won't interfere with the baseboard heaters, and will form a cohesive look. I'm assuming the curtains will all be the same length.

Your gut is right. They should both be at the same height. And it's is a good idea to keep the material away from the heat register.

Just patch the old holes and if you want some help hanging the rod, here's a article for hanging a valance (so it stays up) but it has some great tips that will apply for hanging a rod.

Here is a link that might be useful: 6 easy tips to hang a valance

I was just going to recommend that very thing - we have a window right next to a large patio door, and the tops of the windows are not aligned, yet they are on the same wall with only 8" separating them, so it looked strange. We used the same solution - curtains rods up as close to the ceiling as you can get them, curtains to the floor (in your case they will be decorative only, with the baseboard heaters). Then the shades will be functional for light control and privacy and in addition disguise the difference in height between the top of the window and the curtain rod. It's a very nice look and completely disguised the uneven windows.

The curtain and bamboo shade combination is one of my favorites, because it can be tweaked to suit everything from coastal cottage to sleek urban traditional to angular modern design, depending on the material and tone of the blinds and the fabric, construction, and hardware of the curtain panels.

And it is the clear choice for windows of uneven heights.

Will you ever be closing the drapes? Are both wall heaters set back from the window edge like the unit on the right wall? Are the heating units water or electrical?
If the heaters are set back from the window edge, I'd hang full length panels if you aren't going to draw them closed. And if the heaters are water there is very little chance of fire, altho heat output will be affected/redirected by drapes.

Yes, you want the rods the same height, and if you choose to go with shorter drapes, make them the same length along the bottom. The window sill on the right looks to be a little lower so, IMO, the bottom of the drapes on the left should be the at the same level as the drapes on the right.

Thanks for the help all. And thanks Annz, you answered the question I had on my mind this morning about the bottom length. Unfortunately these are electric units and put out some heat so I'd like them as far away as I can get them so they'll have to be short but I will make them all the same length. I think the Roman shade will be just the ticket over there.

I have a wide window of 140 inches along a whole wall. I also have the heating system underneath the windows all along the same wall. My problem is that the box where the heating system is does not run even along the wall, where the curtains finish. Half the window box sill is higher and half is lower. I dont know how to hang my curtains with regards to the length. Any ideas please?

You probably should start your own thread, but either way, can you post a picture of your window?