Excuse me while I rain on the Fan Pier victory parade.

Vertex Pharmaceuticals’ decision to build a new headquarters at Fan Pier, so faithfully transcribed by our local media, would seem like a big win for Boston Mayor Thomas M. Menino.

After all, Boston’s mayor for life has struggled for the better part of a generation, literally, to get development underway on South Boston’s half-built waterfront. But dig a little and you will find some big problems with this much trumpeted – but little examined – deal.

First and foremost is Vertex’s tortured relationship with real estate, including a headquarters project in Cambridge from which the company pulled back at the 11th hour.

Then there’s Boston’s move to shower Vertex with tens of millions of dollars in taxpayer subsidies – all to poach a company from neighboring Cambridge.

What happened to at least trying to lure companies from overseas, or, failing that, a somewhat distant state like Kentucky or California?

Never one for a dull quote, Cambridge City Councilor Kenneth Reeves, reacting to the Vertex news, slammed Boston as “the major poacher of them all,” according to the Harvard Crimson.

In 2008, when Vertex first lined up to take down a big piece of the Fan Pier project – which then, as now, was hungrily looking for tenants – I warned about Vertex and its mercurial relationship with real estate on these pages.

Here We Go Again

Of course, it was all sunshine and roses back then, both in the local press and in the pronouncements from city hall. No one was particularly interested in looking backwards – even after Vertex, for a variety of reasons not fully clear, decided to pull back from its Fan Pier deal and renew its lease in Cambridge.

Now, here we go again. Vertex is back on again at Fan Pier, this time with a new and even more substantial deal in the works for 1.1 million square feet of new, custom-built waterfront space.

As I did two years ago, I am happy to dig through my own files, all the way back to 2001. A business reporter for the Boston Herald back then, I picked up what seemed to be a rather bizarre tip.

A fast-growing young biotech had signed a lease for a striking new, 290,000-square-foot glass and steel headquarters in East Cambridge. The company, Vertex, was all set to move in before it balked and pulled back.

It seemed hard to fathom – especially since this was a done deal and the firm was on the hook for millions in lease payments.

But it turned out to be true. Some of Vertex’s drug development programs had not yet produced the results the company – and investors – had hoped for, so the big move was put on hold.

And guess what? That beautiful new research building near Kendall Square sat empty right into mid-2004, when Vertex began subleasing space to other local biotech companies. Vertex did eventually take some floors of its own as well.

OK, that was a decade ago. So what difference does that make now? Let’s fast forward to look at the current deal.

There is a letter of intent to take space at Fan Pier, but no lease yet. That awaits FDA approval – possibly as early as this spring – for a Vertex drug touted as a potentially blockbuster treatment to combat hepatitis C.

Here again, as was the case a decade ago, Vertex is making a major real estate commitment contingent on a federal regulatory ruling in Washington. This time, though, it was smart enough not to sign the lease in advance.

A lot rides on that FDA ruling. Vertex is on track to report a loss of more than $700 million for 2010. That’s enough to buy a downtown office tower.

‘Regional Benefit’

Now, it’s probably not entirely fair to blame Vertex for the hype surrounding its on-and-off courtship with Fan Pier. The company itself has generally been tight-lipped with the press, and upfront with city officials and developers alike about the contingencies involved. Whether Vertex has what it takes to be an anchor for waterfront development remains to be seen, but its handling of real estate has been typical of a young company experiencing both explosive growth and unpredictable setbacks.

But let’s be generous and say this all comes off without a hitch. Even then, there’s still a cloud over this deal.

What in the world is Boston doing laying out an estimated $60 million in city and state taxpayer dollars to lure a biotech company – and one that has blown hot and cold on real estate deals in the past – from neighboring Cambridge?

I thought that we were all on the same side here in the Bay State – the idea was to keep jobs from flowing to Florida and North Carolina and maybe even poach a few jobs from them from time to time.

First the Evergreen Solar mess, now this? At least with Evergreen, state officials were competing for jobs that later went to China.

Here, taxpayers are shelling out millions to lure jobs across the Charles River. That’s as absurd as it gets.

City hall is now rushing to defend the deal. All that money isn’t being used to lure a company from Cambridge, but rather to ensure it stays here in the Bay State, Boston Redevelopment Authority spokeswoman Susan Elsbree assured me in an e-mail.

“Vertex chose Fan Pier as a place to expand their company, and we’re thrilled they didn’t leave the state,” Elsbree wrote. “We know there will be tremendous regional economic benefit by keeping them here.”

Really? It seems unlikely the research-intensive Vertex was going to bolt a state that has become the place to be for life sciences companies – at worst, it might have migrated to the suburbs.

Nice try, but I’d rather rain on this parade than march in it.