Gary Setchell's 250th game in charge of Lynn ended in a FA Trophy loss after Jake Speight slotted home a controversial 84th-minute penalty.

Referee Anthony Da Costa had been barracked all afternoon for a bemusing display which saw a host of his decisions anger and confuse those in home colours. He turned a couple of decent penalty appeals down for Lynn as the man in black turned what was an ensorbing encounter into a stop-start affair.

Just as it seemed the main gripe would simply be around his poor showing he pointed to the spot after Lynn keeper Alex Street – who appeared to get a hand to the ball – was adjudged to have upended James Walshaw in the closing stages. The fury at his hotly-disputed call only intensified when Speight cooly stroked home to rob lower-level Lynn of the replay they, at the bare minimum, deserved.

An equaliser never arrived and as a result the Conference North outfit now find their name in the hat for Monday's draw while the Linnets' hopes of another memorable Trophy run came to an end at the final qualifying round.

Lynn went into the game knowing they've pushed both of their Step Two opponents they've faced already this term all the way. A 1-0 victory over Hednesford United was followed up by a narrow 4-3 defeat to big-spending AFC Fylde in the FA Cup.

In the Trophy too, the Linnets have already shown they can see off illustrious opponents during a number of exciting runs in national knockout competitions. So hopes were high that the Sulphurites could become the hosts' latest scalp as they looked to progress and pocked £4,000 prize money.

Setchell was handed a pre-game boost with captain David Bell passing a late fitness test to start in the centre of midfield. The only player unavailable was suspended centre-back Henry Eze.

It was a cagey opening with plenty of respect being shown from both parties. Keeper Street's safe handling and quick release sparked the first attacking break of note after almost 10 minutes. The Lynn shot-stopper set Jake Jones away, he charged up field, slotted in Steve Spriggs, and darted into the area where he met the wideman's centre with a header that Phil Barnes turned away at the second time of asking.

Former professional Speight displayed his class to find a pocket of space on the edge of the box at the other end. Yet his effort looked more Sunday League than Football League as it drifted miles off target.

Spriggs' influence down the right, and Jones' on the opposite flank, continued to grow as the Linnets once again more than held their own. It was the former who got to the byline and teed up George Thomson but his drive failed to trouble Barnes.

With opportunities at a premium, the visitors' Luke Sheils and Speight would have been far wiser to communicate at the back post as they both arrived to head at goal. Instead they only collided with each other and the chance was lost.

Around the 20th minute saw the first real spell of sustained pressure as Lynn went seriously close on three occassions. First, a great block from defender Dave McGurk diverted Spriggs' drive wide. From the resulting corner, Gregg Smith's header drifted past the top corner – and the ready-to-pounce Spriggs.

And then only a few moments of brilliance, and bravery, from Harrogate's number one, kept the scores at 0-0. Jones found the on-running Spriggs and his wicked effort across goal was palmed away expertly. But Barnes' work wasn't done as he had to leap to his feet to prevent Thomson, Jones and Smith – with a little help from a few colleagues – from netting in the ensuing goalmouth scramble.

A period of inactivity, in either box, continued until the 40th minute when Lloyd Kerry's inviting centre was held well by Street. Youngster Shaun Stocker then followed suit by shutting out Speight with an excellent covering tackle from right back.

But the rest of the half was all about referee Da Costa's increasing ability to irritate all connected with the Linnets thanks to a host of strange decisions that disrupted the rhythm of proceedings. He was booed off at the break as the teams went in deadlocked.

Lynn started the second period on the front foot with Ryan Fryatt's header back across goal, after Bell's delicate centre, eventually finding Ross Watson. But his thumping shot was blocked by a body in blue.

Thomson's clever daisy-cutting free-kick went under the wall but just the wrong side of the post as Setchell's charges searched for a way through. Bell went almost as close as he nearly finished off a sweet move involving Fryatt and Thomson but could only screw wide.

Thomson outstripped Leigh Franks and went over under pressure but despite noisy home appeals the man in the middle waved play on. Even if he appeared to make the most of it, you can argue that you've seen them given. More cries for a spot-kick followed when Smith hit the deck but this time it looked like Sheils had won the ball fairly.

As the noise levels increased you could almost sense Lynn's belief and drive increasing further. They looked the likelier of the two teams on show to make a breakthrough. But it was hearts in mouth when a free-kick, flicked on inadvertedly by Jordan Yong, was crashed just over by Walshaw from the middle of the danger zone.

While there were no goals, the tie remained intriguing and delicately poised. As the clock edged towards the last 15 minutes, you could sense an air of nervousness growing.

A flashpoint between Fryatt and Speight, who went head-to-head off the ball, further raised tensions. But some sensible refereeing from Da Costa ensured both men were just given a talking to rather than being dismissed.

His next call was far less pleasing though as Walshaw went down and Street was punished. Speight made no mistake and that was that for Lynn's Trophy dreams this season.

Lynn (4-4-1-1): Street, Stocker (Mulready, 90), Watson (Frew, 85), Fryatt, Yong, Spriggs, Bell, Bridges, Jones (Quigley, 74), Thomson, Smith. Subs not used: Ramm, Colman. Booked: Smith. Goal: None.

Harrogate (3-5-2): Barnes, Turner, Meynell, Franks (Nelthorpe, 60), Sheils, McGurk, Kerry, Nowakowski, Speight (Bloomer, 87), Walshaw (Swain, 90), Dean. Subs not used: Metcalfe, Crook. Booked: Nowakowski, Dean, Sheils. Goal: Speight (84, pen).

Referee: A. Da Costa

Attendance: 719