What happens if you switch those 2003 processed images over to the 2010 or 2012 process?
Just because you started with the 2003 process doesn't mean you have to stay with that process.
In fact as the Process version has updated I always switch to the newest process for all my images.
I see no difference in the PV2012 and PV2003 gradient, but PV2003 is slightly darker than PV2012 with the default settings. Did you use a monitor calibrator both with PV2003 images and PV2012 images with the same Luminance setting, for example 100 cd/m2? If not your monitor may have been adjusted to a different brightness (i.e. higher) with the PV2003 images, or perhaps you are now using a different monitor. When reviewing older images that were process using PV2003 or PV2010 there's no need to update them unless you're not happy with the way they look. In general images that have a high dynamic range (bright highlights and very dark shadows) will benefit from using PV2012.
Since you aren't happy with these PV2003 images I suggest updating them to PV2012 using the Update tool (lightning bolt) in the Histogram:
I made a few snapshots (German user interface):
Lightroom 6.8 - process 2003 (same look in process 2010 - so my first post was not fully correct):
Lightroom 6.8 - process 2012:
Changing from process 2012 to 2010 or 2003, the picture (sky) is dark again.
Lightroom 4.4 - process 2003:
Of course, I could change the process - but the problem will remain wiithin the software.
Can you post this image or another image file that exhibits the issue to Dropbox or other file sharing site? Please Export and upload the file in DNG format, which will contain your Develop settings.
I can confirm what you are seeing. Below is the IMGP8729.dng downloaded image file with no additional changes applied in LR 4.4.1 and CC 2015.8 (latest version). We do expect to see changes when updating a PV2003 image to PV2012, but that's not what you are doing. Image files that have been edited in PV2003 in older versions of LR (i.e. LR 4) should look identical when merely "viewed" in a newer version of LR. There were major changes made in PV2012 and the Clarity strength was increased significantly. It appears that when viewing a PV2003 image file in LR 6/CC 2015 it is applying PV2012 Clarity in the Local controls (i.e. Graduated Filter).
I suggest reporting this as a 'Problem' at the Photoshop Family forum here: Photoshop Family Customer Community Please reference this post and place the URL link into your report. Also place the URL link for you report in this post (cross-link). Thank you!
EDIT: I had a chance to check if this was already reported and found a post with a similar issue: Lightroom 2015.8: Clarity Issue | Photoshop Family Customer Community I have added your issue to the report so let's see if we get a response back from Adobe Rep Rikk Flohr.
Lightroom 4.4.1 (top), LR CC201.8 (bottom)
So let's hope that the issue gets fixed.
Thank you for your support!