Make a test copy of your cfc. Start invoking it and dumping data until you can see the line of code that is stripping away your zeros.
I am actually just now having the same problem. I don't know of a good solution so I put in a conditional to add a space if the string starts with zero.
<cfif left(.getValue.value,1) EQ '0'>
<cfset arrayAppend(row["cell"], ' #local.getValue.value#')>
<cfset arrayAppend(.row["cell"], local.getValue.value)>
If you are using CF 9.0 there was a documented bug that has been fixed in Adobe® ColdFusion® 9.0 Update 1:
When you use serializeJSON or deserializeJSON, data type conversion occurs automatically. For example, 000001 is converted to numeric 1.
I know that there are new bugs introduced with Updater 1 so it would probably be wise to get the ColdFusion 9.0.1 Cumulative Hot Fix 1 also. As always, test the updates before using in production.