**UPDATE** 2/17/2014
So in the past few days, Nijie has gone and changed things around again.
Basically, clicking the images no longer leads to the direct image, but a "pop-up" similar to pixiv. That's all fine and dandy but they added one more little "feature", namely lite versions of images.
Let's use http://nijie.info/view_popup.php?id=73763 as an example. The image loaded here is http://pic04.nijie.info/small_light%28q=40%29/nijie_picture/6908_20140217213952.jpg and as you can see, it is pretty badly jpeg artifacted. Notice the small_light(q=40) section of the link, this determines the compression level of the image loaded. 40 seems to be the common default.
Fortunately, removing that part leads to the original image, like so http://pic04.nijie.info/nijie_picture/6908_20140217213952.jpg. Notice the difference in sizes: the lite version is 53.73 KB (55015 bytes) while the original is 685.53 KB (701979 bytes). That's quite a huge difference there.
For PNGS (http://pic04.nijie.info/small_light%28q=40%29/nijie_picture/40650_20140217200552.png vs http://pic04.nijie.info/nijie_picture/40650_20140217200552.png) this actually INCREASES the file size.
For now, removing the small_lite(q=40) section works just fine, but who knows how much longer that will be the case. I've looked around the settings as best I could and did not notice any options to change this. If anyone with better Japanese skills can give a proper look, please do so.
**END UPDATE**
At some point in time most, if not all, pngs on the site at the time were converted to JPG. For example: http://nijie.info/view.php?id=4878 and post #971426
The easiest way to tell this has happened is to check the image's direct URL on nijie. From the top example, http://pic01.nijie.info/nijie_picture/4148_4878_1338201816.jpg.
If you run into a URL in that format (####_####_##########.jpg), then it was most likely a png before being converted.
The original URL would have been a single, long series of numbers with no breaks(################.png, though recently this was changed to ####_######### as the new default. Images with multiple versions on the page will be #_###_###_#########, http://nijie.info/view.php?id=25285 for example.)
Antoher way to tell is the dithering applied to the image during the conversion. Again, look closely at the above Nijie example.
Looking through source:*nijie.info/nijie_picture/*_*_*, I've found a few images that were uploaded after being converted: post #1240112 post #1240118 post #1240779 post #1256658 post #1263293 and post #1204000.
If you look closely on all of them, you'll notice the dithering applied to them after being converted. This is especially obvious with post #1263293 and its parent, post #933899.
Phew, okay, I'm terrible at explaining things but hopefully I got my point across: Be careful when uploading older images from Nijie, as it might have originally been a png that was converted.
As to why and when, exactly, Nijie did this, I have no idea. What's even more mysterious is the original images are actually still on Nijie's servers. It could be possible to contact Nijie's staff and let them know of the problem and hopefully have them revert the images to their original state.
Updated