We are hitting a wrong ordering in 5.2.10 but it does not happen on a test box using 5.3 series (tried 5.3.3 and 5.3.5).
The query can be rewritten and when we do, the range becomes an index scan and produces the correct results.

Here are the queries:
[Incorrect Order]
SELECT SUBSTRING(StockNo, 3, 3) AS $number FROM inv WHERE StockNo LIKE
'JR%' OR StockNo LIKE 'VS%' OR StockNo LIKE 'JB%' OR StockNo LIKE 'JG%'
ORDER BY $number DESC LIMIT 1;

EXPLAIN Result

id	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
1	SIMPLE	inv	range	PRIMARY	PRIMARY	66	(NULL)	4	Using where; Using index; Using filesort

[Correct Order]
SELECT SUBSTRING(StockNo, 3, 3) AS $number FROM inv WHERE LEFT(StockNo,2) IN('JR','VS','JB','JG')
ORDER BY $number DESC LIMIT 1;

EXPLAIN Result

id	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
1	SIMPLE	inv	index	(NULL)	PRIMARY	66	(NULL)	2496	Using where; Using index; Using filesort

Simplified Table Structure:
CREATE TABLE `tableinventory` (
`StockNo` varchar(64) NOT NULL DEFAULT '',
`ItemDesc` varchar(96) NOT NULL DEFAULT '',
PRIMARY KEY (`StockNo`)
) ENGINE=PBXT DEFAULT CHARSET=latin1;

All data is using a length of 7 even though it is defined as varchar(64).