The behavior you describe is as expected. See this site for detailed confirmation. You may also want to review the description here.
Since DST is ending in the fall, and the clocks move backwards, we call this the "fall back" transition. As your clock is approaching 2:00 AM, it falls back to 1:00 AM instead. The local time from 1:00:00 to 1:59:59.999 is repeated. By the time 2:00 hits, it's already repeated the second instance of the 1:00 hour and DST is well over.
We use the label EDT for Eastern Daylight Time, when the offset is at UTC-04:00, and the label EST for Eastern Standard Time, when the offset is at UTC-05:00. So no, EDT and EST are not the same. It does matter which one you are in, especially during the 1:00 hour on the day of the transition.
The clock advances like this:
...
00:59:58 EDT (-0400)
00:59:59 EDT (-0400)
01:00:00 EDT (-0400) --+
01:00:01 EDT (-0400) |--- 1st instance of 1:00 hour
... |
01:59:59 EDT (-0400) --+
01:00:00 EST (-0500) --+ <---- transition
01:00:01 EST (-0500) |
... |--- 2nd instance of 1:00 hour
01:59:59 EST (-0500) --+
02:00:00 EST (-0500)
02:00:01 EST (-0500)
...
Also keep in mind that when you set the time to 1:00 local time, you aren't being specific enough. Since there are two instances of 1:00, the OS will just pick one for you. On Linux and Mac OSX the underlying system clock is kept in UTC. 1:00 EDT is at 5:00 UTC, while 1:00 EST is at 6:00 UTC.
Restarting your machine should have no effect. My guess is that you didn't restart it right away, but allowed the time to elapse so it moved backward again.
Additional Info
Take a look at the man page for the date
command. We can set the clock by the local time, using the somewhat strange format of [[[mm]dd]HH]MM[[cc]yy][.ss]
So this is 1:00 local time on the day of the transition:
date 110301002013
But that is not very specific, so the OS is probably picking EDT because it's the first instance. It might as well pick EST though, since we didn't specify.
Instead, consider setting it by UTC:
date -u 110305002013 (1:00 EDT)
or
date -u 110306002013 (1:00 EST)