Mobs and objs with an initial pixel offset did not show correctly, until they updated, when older clients connected to a server running version 489.
BYOND Version:489
Operating System:Windows Vista Home Premium 64-bit
Web Browser:Firefox 5.0.1
Applies to:Dream Seeker
Status: Resolved (490)

This issue has been resolved.
Descriptive Problem Summary:
Pixel offset is acting strangely for clients connecting using BYOND 488 to a BYOND 489 server. In NEStalgia every player and NPC has a pixel_y offset of 8, just defined like this:

pixel_y = 8

I've been compiling using BYOND 489 for a couple weeks now, but I didn't upgrade the Dream Daemons for NEStalgia servers to 489 until yesterday. Shortly afterwards, players started seeing NPCs and players with no pixel offset at all. The visual glitch was limited to players using 488 or lower to connect, and the pixel_y offset seems to fix itself randomly (usually when the player moves or teleports). Screenshots and details can be found in this thread:

Having the client upgrade to BYOND 489 fixes the issue, but I figured that you should be aware of it.