It seems that when accessing tables with 1 column, the action of accessing throws away the column information. This information is kept if there is more than 1 column.
E.g.
With 1 item in the table:
> example1 <- data.frame( items = c("A","B","B","C","C","C","C")
+ , time = ISOdate(2222,1,1) )
> table1 <- table(example1)
> table1
time
items 2222-01-01 12:00:00
A 1
B 2
C 4
> barplot(table1, legend=T)
> table1.ordered <- table1[c(3,2,1),] # reorder
> table1.ordered
C B A
4 2 1
> barplot(table1.ordered, legend=T) # time column thrown away
Now with 2 items in table: (added onto example1 in this example)
> example2 <- rbind(example1 , data.frame(items = NA, time = ISOdate(3333,1,1)) )
> example2
items time
1 A 2222-01-01 12:00:00
2 B 2222-01-01 12:00:00
3 B 2222-01-01 12:00:00
4 C 2222-01-01 12:00:00
5 C 2222-01-01 12:00:00
6 C 2222-01-01 12:00:00
7 C 2222-01-01 12:00:00
8 <NA> 3333-01-01 12:00:00
> table2 <- table(example2)
> table2
time
items 2222-01-01 12:00:00 3333-01-01 12:00:00
A 1 0
B 2 0
C 4 0
> table2.ordered <- table2[c(3,2,1),] #Again, reorder
> table2.ordered
time
items 2222-01-01 12:00:00 3333-01-01 12:00:00
C 4 0
B 2 0
A 1 0
> barplot(table2.ordered, legend=T) #displays how I expected