Is Stencyl changing my sprite colors?

So I have this weird thing happening. First I create my sprites outside of Stencyl(in Pixen, for the Mac; marvelous little app to create bitmap, so far). Then I use the "import from sheet" option in Stencyl to get those sprites into Stencyl and cut them as I see fit(and btw, I'm always frustrated by how I can't specify how many of those sprites I want to actually use; but such is life).

Problems comes when I decide I need to edit something on the sprite. For example, I want to move it a few pixels up or down or reverse it(I usually only draw my sprites going one direction and flip them).

Then I realize either Stencyl is doing something weird with my colors or Pixen is, but it turns out the colors are usually darker and now my animations looks like it's blinking. Same happens for tiles(especially tiles with transparency).

Has anyone seen this before and know if there's a way to avoid it?

(I'll get some pictures to post here later when I arrive home, I just decided to post this here before I forget again)

I have had this happen before but I was never able to find the cause of it. I noticed it more with anything with transparency as you said. If I remember correctly, I think reimporting the animation will fix the problem (at least temporarily). Also try downloading the newest nightly build of Stencyl and see if anything is different.

If you're not saving your images in PNG format, you should.

I only work in PNG. Here are two versions of the same sprite: the first one is the original PNG, the second one was imported in Stencyl and then edited in the same software.

I've never encountered this. Edit your png outside of Stencyl and then import it in. Is this what you're doing?

I create them outside of Stencyl. I wish I didn't have to re-import them every time I do any changes because the only way to do it in Stencyl is either copy-pasting them from the spritesheet or importing the whole spritesheet and deleting the other frames that don't fit.

Or creating one spritesheet for each animation, but I think that undermines the purpose of a spritesheet to some extent.

There definitely needs to be some way to replace/update a sprite sheet by swapping out the physically image file outside of Stencyl and then getting to 'refresh' the spritesheet.  I want to do this a lot - when adding to a tileset, but have to create single tiles and then import them one at a time.

Yep, the tileset is even worse. I get that Stencyl tilesets are actually complex(with collision shapes and what not), but everytime I add a new tile it makes a total mess out of the grid. :/