Not a bug
BYOND Version:512.1462
Operating System:Windows 7 Pro 64-bit
Web Browser:Chrome 71.0.3578.98
Applies to:Dream Seeker
Status: Not a bug

This is not a bug. It may be an incorrect use of syntax or a limitation in the software. For further discussion on the matter, please consult the BYOND forums.
I don't really know what exactly is going wrong but I do believe there's a bug happenning with animating big icons. I've made a simple test case for you that shows it happenning 100% of the times. Link: file

Descriptive Problem Summary:
In the test case, drawing the lighting_plane shouldn't affect the day_night obj's alpha nor color, but the moment the lighting_plane obj is created, the alpha is affected and the color is reseted. Notice how the color changes.

Numbered Steps to Reproduce Problem:
Open the project
Use the verb "draw planes" (notice how it changes the color)
Use the verb "drawspotlight"

Expected Results:
The color and the alpha from daynight should be mantained, and the spotlight
should get throught it, removing it where it is present

Actual Results:
The color and the alpha from daynight are disregarded.

Does the problem occur:
Every time? Or how often? Every time
In other games? Yes
In other user accounts? Yes
On other computers? Yes

When does the problem NOT occur? Never

Workarounds: None that I know of

Can you upload that test to a host that isn't Mediafire? Mediafire has become nigh unusable.
In response to Lummox JR
I haven't forgotten this; I just got pulled way off bug fixes this week.

The download did work okay so I'll check that out soon.
In response to Lummox JR
Nice, just wanted to confirm that the link was good for you. Looking forward for this fix.
Lummox JR resolved issue (Not a bug)
After testing I can confirm there is no bug here. Basically you're doing a number of things wrong with the lighting plane and the day/night loop.

First, you can't be varying the alpha of the lighting plane's backdrop. There always has to be a solid backdrop if you want objects on the lighting plane with alpha to work correctly. This is one of the reasons the alpha on the spotlight doesn't look right.

Once I set the alpha to 255 all the time, the translucent parts of the spotlight still appear to change color. However, this is because you're adding a small amount of white to either a darker or lighter color, and the difference is pretty noticeable. One way to avoid this is to use a color matrix on the backdrop instead of a straight color.

// here r,g,b are from 0 to 1, not 0 to 255, so adjust accordingly
color = list(1-r,0,0, 0,1-g,0, 0,0,1-b, r,g,b)

That matrix will "scale down" all the spotlights so you still have a gradual fade between full white and the background color.

Another issue in the code is that day_night_loop() is just plain wrong. You should simply set the animation when the object is first created, and not have a looping proc at all. It'd look like this:

animate(src, color=NIGHT_MATRIX, time=12000, easing=SINE_EASING, loop=-1)
animate(color=DAY_MATRIX, time=12000, easing=SINE_EASING)

That's all there is to it. A proc doesn't need to run at all.
In response to Lummox JR
If I can't fiddle with the alpha then I don't know of a proper way to use a day and night system because it'll either be too colorfull at day or too dark at night. The only way I knew of how to balance that was with the alpha on the daynight obj.
That's why you need a matrix as I suggested. You can get the multiplication you want and still have a nice fade from the white.