[R] Procedure not working for actual data

[LCOG1]

Hello all, 
   I have what i feel is a unique situation which may not be resolved with
this inquiry.  I have constructed the below data set so that i may give an
example of what im doing.  The example works perfectly and i have no issues
with it.  My problem arises with my actual data, which includes another 11
columns of data (used in later analysis) and a total of about 7000
cases(rows).  i mention the dimensions of the actual data because im
wondering if my below process would encounter problems with more data.
  To be sure the problem occurs in the last step.  Is$NotTooSmall gives me a
binary output that is then put back in MultiLotBldgs.. (as shown in the
example) to return the cases i want to keep. 
 In my actual data the binary designation is correct but when
MultiLotBldgs2.. returns it doesnt remove the cases that are False in 
Is$NotTooSmall.  Like i said my sample data works fine but my actual
implementation does not.  Any suggestions?  I know this is not easy to
answer without seeing the problem but this is the best i can do without
sending you all of my data.  

Cheers, 
JR




#Sample data
Bldgid<-c(1000,1000,1001,1002,1003,1003)
Maplot<-c(20000,20001,30000,30001,40000,40001)
Area<-c(40,170,50,100,100,4.9)
#Construct Sample dataframe
MultiLotBldgs..<-data.frame(Bldgid,Maplot,Area)
#Get Building Areas
MultiLotBldgArea.X <- unlist(tapply(MultiLotBldgs..$Area,
MultiLotBldgs..$Bldgid, 
                              function(x) x))

# Calculate the proportion of the total building area in each piece of the
building
MultiLotBldgProp.X <- unlist(tapply(MultiLotBldgs..$Area,
MultiLotBldgs..$Bldgid, 
                              function(x) x/sum(x)))

#Identify buildings that should be considered for joining
Is$NotTooSmall.X <- !(((MultiLotBldgArea.X <= 45) | 
                            ((MultiLotBldgArea.X > 45) & (MultiLotBldgProp.X
< 0.05))))

MultiLotBldgs2.. <- MultiLotBldgs..[Is$NotTooSmall.X, ]

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