I think this has already been covered enough in this thread, but I'll throw in my two cents anyway.
If the Houses had cloaking technology only they kept it secret from non-military factions, as someone here suggested, Juni would not have been so shocked -- she is LSF. While that does not immediately mean that she must know of all secret government projects, it is possible that she was high-ranking enough to at least have heard rumours, if not been contracted to defend the secret once or twice. And she did know of experiments with the technology, going some way to prove the point.
Someone else said that Starlancer's cloaks probably wouldn't be considered true cloaks anymore. I think that's an accurate guess. They weren't too hard to spot then, 800 years on I'm sure sensors would have advanced more than enough to see them too. And they hadn't managed to cloak something as large as a capital ship, so there would still be an element of shock. And thus if this is the case, then the cloaking technology Juni is so surprised to see would be totally new; you can neither see nor detect it. And the fact that this would seem to require huge amounts of power (10 battleship cores, does a rumour somewhere suggest?) goes some way to demonstrating how effective sensors in Sirius have become.
If this is not the case, there are two other options:
1) The data on the cloaks developed by the Coalition and the Alliance had not been included on the sleeper ships. I would go with this one; there would be so much information to include on their computer data banks that cloaking their ships in a place where there were no enemies would not be a priority.
2) The data was included on the sleeper ship computers, but the computer records degraded in transit. Now if they still use MS Windows by then, this would be more likely than option 1. And I'm sure that their data banks did suffer some level of degredation. But I would assume this, although likely, to be less likely than the former.
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